From 77286807f3559796a57b985faaf4b0b0337ddfff Mon Sep 17 00:00:00 2001
From: Cedric Notredame <cedric.notredame@gmail.com>
Date: Tue, 20 Feb 2024 17:29:52 +0100
Subject: [PATCH] replaced the most problematic occurences of europe.com

---
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 ....crg.es's conflicted copy 2016-05-05).html | 193 ---------
 ...crg.es's conflicted copy 2016-05-05).html~ | 177 --------
 public_html/Courses/Exercises/index.html      |   2 +-
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 public_html/Courses/Exercises/index.html~     | 346 ---------------
 .../Courses/anonymous_sequence/index.html     |   2 +-
 public_html/Documentation/align_pdb.doc.txt   |   2 +-
 public_html/Documentation/aln_compare.doc.txt |   2 +-
 public_html/Documentation/analyse_pdb.doc.txt |   2 +-
 public_html/Projects/blastr/index.html        |   2 +-
 public_html/Projects/expresso/index.html      |   2 +-
 public_html/Projects/mcoffee/index.html       |   2 +-
 public_html/Projects/mocca/index.html         |   4 +-
 public_html/Projects/procoffee/index.html     |   2 +-
 .../procoffee/procoffee_home_page_old.html    |   2 +-
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 public_html/Projects/robusta/index.html       |   2 +-
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 public_html/Projects/saracoffee/index.html    |   2 +-
 ....crg.es's conflicted copy 2016-05-05).html | 381 -----------------
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 ....crg.es's conflicted copy 2016-05-05).html | 385 -----------------
 ...crg.es's conflicted copy 2016-05-05).html~ | 381 -----------------
 public_html/Projects/tcs/index.html.old       | 320 --------------
 public_html/Projects/tcs/index.html.old2      | 317 --------------
 public_html/Projects/tcs/index.html.old3      | 379 -----------------
 public_html/Projects/trmsd/index.html         |   2 +-
 public_html/Projects/trmsd/index.html~        | 287 -------------
 public_html/Publications/Pdf/all.txt          |  38 +-
 public_html/Resources/book_list.html          |   2 +-
 public_html/Resume/resume.html.old            |   2 +-
 public_html/Resume/resume.txt                 |   2 +-
 public_html/Tcoffee.htm                       |   4 +-
 public_html/Workshops/RNG/list.cvs            |   2 +-
 public_html/Workshops/RNG/x                   |   2 +-
 public_html/Workshops/index.html              |   2 +-
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 public_html/homepage.html                     |   2 +-
 public_html/homepage.html~                    | 402 ------------------
 public_html/index_cnrs.html                   |   4 +-
 public_html/index_sib.html                    |   4 +-
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 47 files changed, 53 insertions(+), 4780 deletions(-)
 delete mode 100755 public_html/Books/index.html~
 delete mode 100755 public_html/Courses/Exercises/index (palestine.crg.es's conflicted copy 2016-05-05).html
 delete mode 100755 public_html/Courses/Exercises/index (palestine.crg.es's conflicted copy 2016-05-05).html~
 delete mode 100755 public_html/Courses/Exercises/index.html.old
 delete mode 100755 public_html/Courses/Exercises/index.html~
 delete mode 100644 public_html/Projects/robusta/index.html~
 delete mode 100755 public_html/Projects/strike/index (palestine.crg.es's conflicted copy 2016-05-05).html
 delete mode 100755 public_html/Projects/strike/index.html~
 delete mode 100755 public_html/Projects/tcs/index (palestine.crg.es's conflicted copy 2016-05-05).html
 delete mode 100755 public_html/Projects/tcs/index (palestine.crg.es's conflicted copy 2016-05-05).html~
 delete mode 100644 public_html/Projects/tcs/index.html.old
 delete mode 100755 public_html/Projects/tcs/index.html.old2
 delete mode 100755 public_html/Projects/tcs/index.html.old3
 delete mode 100755 public_html/Projects/trmsd/index.html~
 delete mode 100644 public_html/Workshops/index.html~
 delete mode 100644 public_html/homepage.html~
 delete mode 100755 public_html/saltt/index.html~

diff --git a/public_html/Books/index.html b/public_html/Books/index.html
index e6845dd..8c0fabb 100755
--- a/public_html/Books/index.html
+++ b/public_html/Books/index.html
@@ -107,7 +107,7 @@ <h2><font color="#0000EE">Compiled By Cedric Notredame</font></h2>
 	 
 	  <table>
 	  
-   <p><font size="2">Questions should be sent to <a href="mailto:cedric.notredame@europe.com">C.Notredame</a> </font></center>
+   <p><font size="2">Questions should be sent to <a href="mailto:cedric.notredame@gmail.com">C.Notredame</a> </font></center>
 </center>
  </body>
  </html>
diff --git a/public_html/Books/index.html~ b/public_html/Books/index.html~
deleted file mode 100755
index 86f17f0..0000000
--- a/public_html/Books/index.html~
+++ /dev/null
@@ -1,41 +0,0 @@
-<html>
- <head>
-  <meta http-equiv="content-type" content="text/html;charset=iso-8859-1">
-  <meta name="generator" content="Adobe GoLive 4">
-  <title>Bioinformatics Workshops</title>
- </head>
- <BODY TEXT="#000000" BGCOLOR="#FFEEDD" LINK="#0000EE" VLINK="#551A8B" ALINK="#FF0000">
- 
- <center>
-      <table border=10 cellpadding="20" width=40% nosave>
-	<tr>
-	  <td align=center bgcolor="FFCCAA">
-	    <h2>Bioinformatics<BR><BR>Schools and Workshops</h2>
-	    <h2><font color="#0000EE">Cedric Notredame</font></h2>
-	  </td>
-	</tr>
-      </table>
-      <br><br><br>
-      
-      <center>
-	<table BGCOLOR="#FFFFEE" Align="center" cellpadding=30  leftmargin="30" marginwidth="30" width="60%"  border="5"> 
-	  <tr>
-	    <th BGCOLOR="#FFDDAA"><h2>Workshops Archives</h2></th>
-	  </tr>
-	  <tr align=center>
-	    <td><font size=+1>SwissProt T-Coffee Workshop, Geneva, April 2006</td>
-	  </tr>
-	  <tr align=center>
-	    <td><font size=+1><A HREF="./RNG/jrng.html">Réseau National des Génopoles (Phylogeny), Marseille, December 2005</a></td>
-	  </tr>
-	  
-          <tr align=center>
-	    <td><font size=+1><A HREF="./prosite_workshop/index.html">Prosite Workshop, Marseille, July 2001, July 2002</a></td>
-	  </tr>
-	</table>
-       <BR><BR>
-
-   <p><font size="2">Questions should be sent to <a href="mailto:cedric.notredame@europe.com">C.Notredame</a> </font></center>
-</center>
- </body>
- </html>
diff --git a/public_html/Courses/Exercises/index (palestine.crg.es's conflicted copy 2016-05-05).html b/public_html/Courses/Exercises/index (palestine.crg.es's conflicted copy 2016-05-05).html
deleted file mode 100755
index 490e2ac..0000000
--- a/public_html/Courses/Exercises/index (palestine.crg.es's conflicted copy 2016-05-05).html	
+++ /dev/null
@@ -1,193 +0,0 @@
-<html>
- <head>
-  <meta http-equiv="content-type" content="text/html;charset=iso-8859-1">
-  <meta name="generator" content="Adobe GoLive 4">
-  <title>Bioinformatics Exercises</title>
- </head>
- <BODY TEXT="#000000" BGCOLOR="#FFEEDD" LINK="#0000EE" VLINK="#551A8B" ALINK="#FF0000">
- 
- <center>
-      <table border=10 cellpadding="20" width=40% nosave>
-	<tr>
-	  <td align=center bgcolor="FFCCAA">
-	    <h2>Bioinformatics<BR><BR>Courses</h2>
-	    <h2><font color="#0000EE">Cedric Notredame</font></h2>
-	  </td>
-	</tr>
-      </table>
-      <br><br><br>
-      
-      <center>
-	<table>
-	  <tr>
-	    <td><font size=+1><a HREF="http://www.amazon.com/gp/product/0470089857?ie=UTF8&tag=wwwtcoffeeorg-20&linkCode=as2&camp=1789&creative=9325&creativeASIN=0470089857" target="_blank">
-		  <img border=0 src="../../logo_dir/cover.jpg" alt="Bioinformatics for dummies"></a></td>
-	    <td><A HREF="http://www.amazon.com/gp/product/0470089857?ie=UTF8&tag=wwwtcoffeeorg-20&linkCode=as2&camp=1789&creative=9325&creativeASIN=0470089857" target="_blank">Bioinformatics for Dummies</a> Can be Used as a Support Book with All the Following Courses. Some of its ressources are available <a href="http://www.dummies.com/WileyCDA/DummiesTitle/productCd-0470089857,page-1.html" target="_blank">Online</a>.</td>
-	  </tr>
-	</table>
-	<br><br>
-            
-      <center>
-	<table BGCOLOR="#FFFFEE" Align="center" cellpadding=30  leftmargin="30" marginwidth="30" width="60%"  border="5"> 
-		      
-
-
-
-
-		      <tr>
-			<th BGCOLOR="#FFDDAA"><h2>Available Ressources</h2></th>
-		      </tr>
-		      
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./madrid_2014/index.html">Introduction to Pairwise 
-			      and Multiple Sequence Alignments, Madrid, November 2014</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ma_2014/index.html">Introduction to Multiple Sequence Alignments, UPF, October 2014</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ug_2014/index.html">Introduction to Sequence Comparison, UPF, October 2014</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./bologna_ma_2014/index.html">RNA Analysis,Bologna,September 2014</a></td>
-			</tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./uab_ma_2013/index.html">Sequence Comparison, UAB, November 2013</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./madrid_2013/index.html">Introduction to Pairwise 
-			      and Multiple Sequence Alignments, Madrid, November 2013</a></td>
-		      </tr>
-
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ug_2013/index.html">Introduction to Sequence Comparison, UPF, October 2013</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./bologna_ma_2013/index.html">RNA Analysis,Bologna,September 2013</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./vic_ma_2013/index.html">Sequence Comparison, VIC, March 2013</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./uab_ma_2012/index.html">Sequence Comparison, UAB, November 2012</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./madrid_2012/index.html">Introduction to Pairwise 
-			      and Multiple Sequence Alignments, Madrid, November 2012</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ma_2012/index.html">Introduction to Multiple Sequence Alignments, UPF, October 2012</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ug_2012/index.html">Introduction to Sequence Comparison, UPF, October 2012</a></td>
-		      </tr>
-
-
-		      <tr align=center>
-			<td><font size=+1><A HREF="./madrid_2011/index.html">Introduction to Pairwise 
-			      and Multiple Sequence Alignments, Madrid, November 2011</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ma_2011/index.html">Introduction to Multiple Sequence Alignments, UPF, October 2011</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ug_2011/index.html">Introduction to Sequence Comparison, UPF, October 2011</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./Bilbao_2011/index.html">Introduction to Multiple Sequence Alignments, Bilbao, July 2011</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./Tangier_EMBO_2011/index.html">Introduction to Protein Sequence Alignments (Multiple and Pairwise), EMBO Course, Tangier, June 2011</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./madrid_2010/index.html">Introduction to Pairwise 
-			      and Multiple Sequence Alignments, Madrid, November 2010</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ma_2010/index.html">Introduction to Multiple Sequence Alignments,UPF,October 2010</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./saragosa_pb_2010/index.html">Introduction to Multiple Sequence Alignments,Saragosa,April 2010</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ug_2010/index.html">Introduction to Sequence Comparison, UPF, January 2010</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./madrid_2009/index.html">Introduction to Pairwise and Multiple Sequence Alignments, Madrid, November 2009</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ma_2009/index.html">Introduction To Multiple Sequence Alignment,UPF, October 2009</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ug_2009/index.html">Introduction to Sequence Comparison, UPF, January 2009</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./madrid_2008/index.html">Introduction to Pairwise and Multiple Sequence Alignments, Madrid, November 2008</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_2008/index.html">Introduction To Multiple Sequence Alignment,UPF, October 2008</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_2007/index.html">Introduction To Multiple Sequence Alignment,UPF, November 2007</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./madrid_2007/index.html">Introduction To Multiple Sequence Alignment,Madrid, November 2007</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./sardinia_07/index.html">Introduction To Sequence Analysis, Polaris (Italy), May 2007</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="../anonymous_sequence/index.html">An Anonymous Sequence for the Online Supplement of Bioinformatics For Dummies</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./pavie_07/index.html">Introduction To Perl, February 2007</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./bergin_06/index.html">Introduction To Sequence Analysis, Bergin (Norway), May 2006</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./sardinia_06/index.html">Introduction To Sequence Analysis, Polaris (Italy), May 2006</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./bgp_2001/index.html">Cell Biology, Lausanne (Switzerland), December 2001</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./sanbi_course_00/exercises.html">Sanbi, Johanesburg, Capetown (SA), November 1999</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./EmbnetCourse_99/problems.html">EMBnet, Lausanne (Switzerland), September 1999</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./turkey_00/exercises.html">Introduction to bioinformatics (Exercises)</a></td>
-		      </tr>
-		      
-		      <tr align=center >
-			<td><font size=+1><A HREF="./Maln/index.html">Multiple Alignments (Course + Exercises)</a></td>
-		      </tr>
-		      
-		      <tr align=center >
-			<td><font size=+1><A HREF="./Aln/Perl_examples/aln_algorithms.html">Sequence Alignment Algorithms in Perl</a></td>
-		      </tr>
-		      
-		      <tr align=center >
-			<td><font size=+1><A HREF="./SEQ1/seq_list.html">Anonymous Sequences</a></td>
-		      </tr>
-		    </table>
-		    <BR><BR>
-			
-   <p><font size="2">Questions should be sent to <a href="mailto:cedric.notredame@europe.com">C.Notredame</a> </font></center>
-</center>
- </body>
- </html>
diff --git a/public_html/Courses/Exercises/index (palestine.crg.es's conflicted copy 2016-05-05).html~ b/public_html/Courses/Exercises/index (palestine.crg.es's conflicted copy 2016-05-05).html~
deleted file mode 100755
index 65687b9..0000000
--- a/public_html/Courses/Exercises/index (palestine.crg.es's conflicted copy 2016-05-05).html~	
+++ /dev/null
@@ -1,177 +0,0 @@
-<html>
- <head>
-  <meta http-equiv="content-type" content="text/html;charset=iso-8859-1">
-  <meta name="generator" content="Adobe GoLive 4">
-  <title>Bioinformatics Exercises</title>
- </head>
- <BODY TEXT="#000000" BGCOLOR="#FFEEDD" LINK="#0000EE" VLINK="#551A8B" ALINK="#FF0000">
- 
- <center>
-      <table border=10 cellpadding="20" width=40% nosave>
-	<tr>
-	  <td align=center bgcolor="FFCCAA">
-	    <h2>Bioinformatics<BR><BR>Courses</h2>
-	    <h2><font color="#0000EE">Cedric Notredame</font></h2>
-	  </td>
-	</tr>
-      </table>
-      <br><br><br>
-      
-      <center>
-	<table>
-	  <tr>
-	    <td><font size=+1><a HREF="http://www.amazon.com/gp/product/0470089857?ie=UTF8&tag=wwwtcoffeeorg-20&linkCode=as2&camp=1789&creative=9325&creativeASIN=0470089857" target="_blank">
-		  <img border=0 src="../../logo_dir/cover.jpg" alt="Bioinformatics for dummies"></a></td>
-	    <td><A HREF="http://www.amazon.com/gp/product/0470089857?ie=UTF8&tag=wwwtcoffeeorg-20&linkCode=as2&camp=1789&creative=9325&creativeASIN=0470089857" target="_blank">Bioinformatics for Dummies</a> Can be Used as a Support Book with All the Following Courses. Some of its ressources are available <a href="http://www.dummies.com/WileyCDA/DummiesTitle/productCd-0470089857,page-1.html" target="_blank">Online</a>.</td>
-	  </tr>
-	</table>
-	<br><br>
-            
-      <center>
-	<table BGCOLOR="#FFFFEE" Align="center" cellpadding=30  leftmargin="30" marginwidth="30" width="60%"  border="5"> 
-		      
-
-
-
-
-		      <tr>
-			<th BGCOLOR="#FFDDAA"><h2>Available Ressources</h2></th>
-		      </tr>
-
- <tr align=center>
-			<td><font size=+1><A HREF="./uab_ma_2013/index.html">Sequence Comparison, UAB, November 2013</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./madrid_2013/index.html">Introduction to Pairwise 
-			      and Multiple Sequence Alignments, Madrid, November 2013</a></td>
-		      </tr>
-
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ug_2013/index.html">Introduction to Sequence Comparison, UPF, October 2013</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./bologna_ma_2013/index.html">RNA Analysis,Bologna,September 2013</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./vic_ma_2013/index.html">Sequence Comparison, VIC, March 2013</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./uab_ma_2012/index.html">Sequence Comparison, UAB, November 2012</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./madrid_2012/index.html">Introduction to Pairwise 
-			      and Multiple Sequence Alignments, Madrid, November 2012</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ma_2012/index.html">Introduction to Multiple Sequence Alignments, UPF, October 2012</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ug_2012/index.html">Introduction to Sequence Comparison, UPF, October 2012</a></td>
-		      </tr>
-
-
-		      <tr align=center>
-			<td><font size=+1><A HREF="./madrid_2011/index.html">Introduction to Pairwise 
-			      and Multiple Sequence Alignments, Madrid, November 2011</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ma_2011/index.html">Introduction to Multiple Sequence Alignments, UPF, October 2011</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ug_2011/index.html">Introduction to Sequence Comparison, UPF, October 2011</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./Bilbao_2011/index.html">Introduction to Multiple Sequence Alignments, Bilbao, July 2011</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./Tangier_EMBO_2011/index.html">Introduction to Protein Sequence Alignments (Multiple and Pairwise), EMBO Course, Tangier, June 2011</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./madrid_2010/index.html">Introduction to Pairwise 
-			      and Multiple Sequence Alignments, Madrid, November 2010</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ma_2010/index.html">Introduction to Multiple Sequence Alignments,UPF,October 2010</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./saragosa_pb_2010/index.html">Introduction to Multiple Sequence Alignments,Saragosa,April 2010</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ug_2010/index.html">Introduction to Sequence Comparison, UPF, January 2010</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./madrid_2009/index.html">Introduction to Pairwise and Multiple Sequence Alignments, Madrid, November 2009</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ma_2009/index.html">Introduction To Multiple Sequence Alignment,UPF, October 2009</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ug_2009/index.html">Introduction to Sequence Comparison, UPF, January 2009</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./madrid_2008/index.html">Introduction to Pairwise and Multiple Sequence Alignments, Madrid, November 2008</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_2008/index.html">Introduction To Multiple Sequence Alignment,UPF, October 2008</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_2007/index.html">Introduction To Multiple Sequence Alignment,UPF, November 2007</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./madrid_2007/index.html">Introduction To Multiple Sequence Alignment,Madrid, November 2007</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./sardinia_07/index.html">Introduction To Sequence Analysis, Polaris (Italy), May 2007</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="../anonymous_sequence/index.html">An Anonymous Sequence for the Online Supplement of Bioinformatics For Dummies</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./pavie_07/index.html">Introduction To Perl, February 2007</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./bergin_06/index.html">Introduction To Sequence Analysis, Bergin (Norway), May 2006</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./sardinia_06/index.html">Introduction To Sequence Analysis, Polaris (Italy), May 2006</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./bgp_2001/index.html">Cell Biology, Lausanne (Switzerland), December 2001</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./sanbi_course_00/exercises.html">Sanbi, Johanesburg, Capetown (SA), November 1999</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./EmbnetCourse_99/problems.html">EMBnet, Lausanne (Switzerland), September 1999</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./turkey_00/exercises.html">Introduction to bioinformatics (Exercises)</a></td>
-		      </tr>
-		      
-		      <tr align=center >
-			<td><font size=+1><A HREF="./Maln/index.html">Multiple Alignments (Course + Exercises)</a></td>
-		      </tr>
-		      
-		      <tr align=center >
-			<td><font size=+1><A HREF="./Aln/Perl_examples/aln_algorithms.html">Sequence Alignment Algorithms in Perl</a></td>
-		      </tr>
-		      
-		      <tr align=center >
-			<td><font size=+1><A HREF="./SEQ1/seq_list.html">Anonymous Sequences</a></td>
-		      </tr>
-		    </table>
-		    <BR><BR>
-			
-   <p><font size="2">Questions should be sent to <a href="mailto:cedric.notredame@europe.com">C.Notredame</a> </font></center>
-</center>
- </body>
- </html>
diff --git a/public_html/Courses/Exercises/index.html b/public_html/Courses/Exercises/index.html
index 244941e..7c6e63c 100755
--- a/public_html/Courses/Exercises/index.html
+++ b/public_html/Courses/Exercises/index.html
@@ -348,7 +348,7 @@ <h2><font color="#0000EE">Cedric Notredame</font></h2>
 		    </table>
 		    <BR><BR>
 			
-   <p><font size="2">Questions should be sent to <a href="mailto:cedric.notredame@europe.com">C.Notredame</a> </font></center>
+   <p><font size="2">Questions should be sent to <a href="mailto:cedric.notredame@gmail.com">C.Notredame</a> </font></center>
 </center>
  </body>
  </html>
diff --git a/public_html/Courses/Exercises/index.html.old b/public_html/Courses/Exercises/index.html.old
deleted file mode 100755
index 65687b9..0000000
--- a/public_html/Courses/Exercises/index.html.old
+++ /dev/null
@@ -1,177 +0,0 @@
-<html>
- <head>
-  <meta http-equiv="content-type" content="text/html;charset=iso-8859-1">
-  <meta name="generator" content="Adobe GoLive 4">
-  <title>Bioinformatics Exercises</title>
- </head>
- <BODY TEXT="#000000" BGCOLOR="#FFEEDD" LINK="#0000EE" VLINK="#551A8B" ALINK="#FF0000">
- 
- <center>
-      <table border=10 cellpadding="20" width=40% nosave>
-	<tr>
-	  <td align=center bgcolor="FFCCAA">
-	    <h2>Bioinformatics<BR><BR>Courses</h2>
-	    <h2><font color="#0000EE">Cedric Notredame</font></h2>
-	  </td>
-	</tr>
-      </table>
-      <br><br><br>
-      
-      <center>
-	<table>
-	  <tr>
-	    <td><font size=+1><a HREF="http://www.amazon.com/gp/product/0470089857?ie=UTF8&tag=wwwtcoffeeorg-20&linkCode=as2&camp=1789&creative=9325&creativeASIN=0470089857" target="_blank">
-		  <img border=0 src="../../logo_dir/cover.jpg" alt="Bioinformatics for dummies"></a></td>
-	    <td><A HREF="http://www.amazon.com/gp/product/0470089857?ie=UTF8&tag=wwwtcoffeeorg-20&linkCode=as2&camp=1789&creative=9325&creativeASIN=0470089857" target="_blank">Bioinformatics for Dummies</a> Can be Used as a Support Book with All the Following Courses. Some of its ressources are available <a href="http://www.dummies.com/WileyCDA/DummiesTitle/productCd-0470089857,page-1.html" target="_blank">Online</a>.</td>
-	  </tr>
-	</table>
-	<br><br>
-            
-      <center>
-	<table BGCOLOR="#FFFFEE" Align="center" cellpadding=30  leftmargin="30" marginwidth="30" width="60%"  border="5"> 
-		      
-
-
-
-
-		      <tr>
-			<th BGCOLOR="#FFDDAA"><h2>Available Ressources</h2></th>
-		      </tr>
-
- <tr align=center>
-			<td><font size=+1><A HREF="./uab_ma_2013/index.html">Sequence Comparison, UAB, November 2013</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./madrid_2013/index.html">Introduction to Pairwise 
-			      and Multiple Sequence Alignments, Madrid, November 2013</a></td>
-		      </tr>
-
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ug_2013/index.html">Introduction to Sequence Comparison, UPF, October 2013</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./bologna_ma_2013/index.html">RNA Analysis,Bologna,September 2013</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./vic_ma_2013/index.html">Sequence Comparison, VIC, March 2013</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./uab_ma_2012/index.html">Sequence Comparison, UAB, November 2012</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./madrid_2012/index.html">Introduction to Pairwise 
-			      and Multiple Sequence Alignments, Madrid, November 2012</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ma_2012/index.html">Introduction to Multiple Sequence Alignments, UPF, October 2012</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ug_2012/index.html">Introduction to Sequence Comparison, UPF, October 2012</a></td>
-		      </tr>
-
-
-		      <tr align=center>
-			<td><font size=+1><A HREF="./madrid_2011/index.html">Introduction to Pairwise 
-			      and Multiple Sequence Alignments, Madrid, November 2011</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ma_2011/index.html">Introduction to Multiple Sequence Alignments, UPF, October 2011</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ug_2011/index.html">Introduction to Sequence Comparison, UPF, October 2011</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./Bilbao_2011/index.html">Introduction to Multiple Sequence Alignments, Bilbao, July 2011</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./Tangier_EMBO_2011/index.html">Introduction to Protein Sequence Alignments (Multiple and Pairwise), EMBO Course, Tangier, June 2011</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./madrid_2010/index.html">Introduction to Pairwise 
-			      and Multiple Sequence Alignments, Madrid, November 2010</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ma_2010/index.html">Introduction to Multiple Sequence Alignments,UPF,October 2010</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./saragosa_pb_2010/index.html">Introduction to Multiple Sequence Alignments,Saragosa,April 2010</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ug_2010/index.html">Introduction to Sequence Comparison, UPF, January 2010</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./madrid_2009/index.html">Introduction to Pairwise and Multiple Sequence Alignments, Madrid, November 2009</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ma_2009/index.html">Introduction To Multiple Sequence Alignment,UPF, October 2009</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ug_2009/index.html">Introduction to Sequence Comparison, UPF, January 2009</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./madrid_2008/index.html">Introduction to Pairwise and Multiple Sequence Alignments, Madrid, November 2008</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_2008/index.html">Introduction To Multiple Sequence Alignment,UPF, October 2008</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_2007/index.html">Introduction To Multiple Sequence Alignment,UPF, November 2007</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./madrid_2007/index.html">Introduction To Multiple Sequence Alignment,Madrid, November 2007</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./sardinia_07/index.html">Introduction To Sequence Analysis, Polaris (Italy), May 2007</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="../anonymous_sequence/index.html">An Anonymous Sequence for the Online Supplement of Bioinformatics For Dummies</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./pavie_07/index.html">Introduction To Perl, February 2007</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./bergin_06/index.html">Introduction To Sequence Analysis, Bergin (Norway), May 2006</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./sardinia_06/index.html">Introduction To Sequence Analysis, Polaris (Italy), May 2006</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./bgp_2001/index.html">Cell Biology, Lausanne (Switzerland), December 2001</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./sanbi_course_00/exercises.html">Sanbi, Johanesburg, Capetown (SA), November 1999</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./EmbnetCourse_99/problems.html">EMBnet, Lausanne (Switzerland), September 1999</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./turkey_00/exercises.html">Introduction to bioinformatics (Exercises)</a></td>
-		      </tr>
-		      
-		      <tr align=center >
-			<td><font size=+1><A HREF="./Maln/index.html">Multiple Alignments (Course + Exercises)</a></td>
-		      </tr>
-		      
-		      <tr align=center >
-			<td><font size=+1><A HREF="./Aln/Perl_examples/aln_algorithms.html">Sequence Alignment Algorithms in Perl</a></td>
-		      </tr>
-		      
-		      <tr align=center >
-			<td><font size=+1><A HREF="./SEQ1/seq_list.html">Anonymous Sequences</a></td>
-		      </tr>
-		    </table>
-		    <BR><BR>
-			
-   <p><font size="2">Questions should be sent to <a href="mailto:cedric.notredame@europe.com">C.Notredame</a> </font></center>
-</center>
- </body>
- </html>
diff --git a/public_html/Courses/Exercises/index.html~ b/public_html/Courses/Exercises/index.html~
deleted file mode 100755
index 4cbff23..0000000
--- a/public_html/Courses/Exercises/index.html~
+++ /dev/null
@@ -1,346 +0,0 @@
-<html>
- <head>
-  <meta http-equiv="content-type" content="text/html;charset=iso-8859-1">
-  <meta name="generator" content="Adobe GoLive 4">
-  <title>Bioinformatics Exercises</title>
- </head>
- <BODY TEXT="#000000" BGCOLOR="#FFEEDD" LINK="#0000EE" VLINK="#551A8B" ALINK="#FF0000">
- 
- <center>
-      <table border=10 cellpadding="20" width=40% nosave>
-	<tr>
-	  <td align=center bgcolor="FFCCAA">
-	    <h2>Bioinformatics<BR><BR>Courses</h2>
-	    <h2><font color="#0000EE">Cedric Notredame</font></h2>
-	  </td>
-	</tr>
-      </table>
-      <br><br><br>
-      
-      <center>
-	<table>
-	  <tr>
-	    <td><font size=+1><a HREF="http://www.amazon.com/gp/product/0470089857?ie=UTF8&tag=wwwtcoffeeorg-20&linkCode=as2&camp=1789&creative=9325&creativeASIN=0470089857" target="_blank">
-		  <img border=0 src="../../logo_dir/cover.jpg" alt="Bioinformatics for dummies"></a></td>
-	    <td><A HREF="http://www.amazon.com/gp/product/0470089857?ie=UTF8&tag=wwwtcoffeeorg-20&linkCode=as2&camp=1789&creative=9325&creativeASIN=0470089857" target="_blank">Bioinformatics for Dummies</a> Can be Used as a Support Book with All the Following Courses. Some of its ressources are available <a href="http://www.dummies.com/WileyCDA/DummiesTitle/productCd-0470089857,page-1.html" target="_blank">Online</a>.</td>
-	  </tr>
-	</table>
-	<br><br>
-            
-      <center>
-	<table BGCOLOR="#FFFFEE" Align="center" cellpadding=30  leftmargin="30" marginwidth="30" width="60%"  border="5"> 
-	    
-	    <tr>
-	      <th BGCOLOR="#FFDDAA"><h2>Available Ressources</h2></th>
-	    </tr>
-	    
-            </tr>
-            <tr align=center>
-	    <td><font size=+1><A HREF="https://docs.google.com/document/d/1CluCrZcuHiLajlYBy-wT4ZluVj9IoVZeWE9cis2qu34/edit">
-		    RNA Analysis, Bologna University, September 2021</a></td>
-	    </tr>
-
-            <tr align=center>
-	      <td><font size=+1><A HREF="./2021_ESCI_ASAB_BDIB_ba/index.html">Algorithm for Sequence Analysis in Bioinformatics, BDIB, ESCI, January 2020</a></td>
-	    </tr>
-	    
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2020_uab_ma/index.html">Sequence Comparison, UAB, November 2020</a></td>
-	      
-	    </tr>
-	    
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2020_crg_ma/index.html">Multiple Sequence Alignments,CRG, November 2020</a></td>
-	      
-	    </tr>
-	    
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2020_upf_ug/index.html">Introduction to Sequence Comparison, UPF, October 2020</a></td>
-	    </tr>
-	    
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2020_bologna_ma/index.html">RNA Analysis, Bologna University, September 2020</a></td>
-
-
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2020_bergen_ma/index.html">Sequence comparison and database search (NORBIS901-Online), May 2020</a></td>
-	    </tr>
-
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2020_ESCI_CMAG_BDIB_ba/index.html">Clustering methods and algorithms in genomics and evolution, BDIB, ESCI, January 2020</a></td>
-	    </tr>
-
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2020_ESCI_ASAB_BDIB_ba/index.html">Algorithm for Sequence Analysis in Bioinformatics, BDIB, ESCI, January 2020</a></td>
-	    </tr>
-	    
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2019_uab_ma/index.html">Sequence Comparison, UAB, November 2019</a></td>
-	      
-	    </tr>
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2019_upf_ma/index.html">Introduction to Multiple Sequence Alignments, UPF, October 2019</a></td>
-	    </tr>
-	    
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2019_upf_ug/index.html">Introduction to Sequence Comparison, UPF, October 2019</a></td>
-	    </tr>
-	    
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2019_bologna_ma/index.html">RNA Analysis,Bologna University,September 2019</a></td>
-	    </tr>
-	    
-	   <tr align=center>
-	      <td><font size=+1><A HREF="./2018_ESCI_CMAG_BDIB_ba/index.html">Clustering methods and algorithms in genomics and evolution, BDIB, ESCI, January 2019</a></td>
-	    </tr>
-
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2018_ESCI_ASAB_BDIB_ba/index.html">Algorithm for Sequence Analysis in Bioinformatics, BDIB, ESCI, January 2019</a></td>
-	    </tr>
-	    
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2018_uab_ma/index.html">Sequence Comparison, UAB, November 2018</a></td>
-	      
-	    </tr>
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2018_upf_ma/index.html">Introduction to Multiple Sequence Alignments, UPF, October 2018</a></td>
-	    </tr>
-	    
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2018_upf_ug/index.html">Introduction to Sequence Comparison, UPF, October 2018</a></td>
-	    </tr>
-	    
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2018_bologna_ma/index.html">RNA Analysis,Bologna University,September 2018</a></td>
-	    </tr>
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2018_ESCI_CMAG_BDIB_ba/index.html">Clustering methods and algorithms in genomics and evolution, BDIB, ESCI, January 2018</a></td>
-	    </tr>
-
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2018_ESCI_ASAB_BDIB_ba/index.html">Algorithm for Sequence Analysis in Bioinformatics, BDIB, ESCI, January 2018</a></td>
-	    </tr>
-	    
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2018_bergen_ma/index.html">Sequence comparison and database search (NORBIS901), Bergen, January 2018</a></td>
-	    </tr>
-	    
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2017_uab_ma/index.html">Sequence Comparison, UAB, November 2017</a></td>
-	      
-	    </tr>
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2017_upf_ma/index.html">Introduction to Multiple Sequence Alignments, UPF, October 2017</a></td>
-	    </tr>
-	    
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2017_upf_ug/index.html">Introduction to Sequence Comparison, UPF, October 2017</a></td>
-	    </tr>
-	    
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2017_bologna_ma/index.html">Introduction to Genome Re-Sequencing, Mapping and Transcriptomic Analysis, Aviano CRO/Bologna University, October 2017 </a></td>
-	    </tr>
-	    
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2016_madrid_ma/index.html">Introduction to Pairwise and Multiple Sequence Alignments, Madrid, November 2016</a></td>
-	    </tr>
-	    
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2016_uab_ma/index.html">Sequence Comparison, UAB, November 2016</a></td>
-	      
-	    </tr>
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2016_upf_ma/index.html">Introduction to Multiple Sequence Alignments, UPF, October 2016</a></td>
-	    </tr>
-	    
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2016_upf_ug/index.html">Introduction to Sequence Comparison, UPF, October 2016</a></td>
-	    </tr>
-	    
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2016_bologna_ma/index.html">RNA Analysis,Bologna,September 2016</a></td>
-	    </tr>
-	    
-	    
-	    
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2015_bergen_ma/index.html">Sequence Comparison, Bergen University, November 2015</a></td>
-	    </tr>
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2015_madrid_ma/index.html">Introduction to Pairwise 
-		    and Multiple Sequence Alignments, Madrid, November 2015</a></td>
-	    </tr>
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2015_uab_ma/index.html">Sequence Comparison, UAB, November 2015</a></td>
-	      
-	    </tr>
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2015_upf_ma/index.html">Introduction to Multiple Sequence Alignments, UPF, October 2015</a></td>
-	    </tr>
-	    
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2015_upf_ug/index.html">Introduction to Sequence Comparison, UPF, October 2015</a></td>
-	    </tr>
-	    
-	    <tr align=center>
-	      <td><font size=+1><A HREF="./2015_bologna_ma/index.html">RNA Analysis,Bologna,September 2015</a></td>
-	    </tr>
-	    
-	    
-	    
-	    
-		      
-	    <tr align=center>
-			<td><font size=+1><A HREF="./madrid_2014/index.html">Introduction to Pairwise and Multiple Sequence Alignments, Madrid, November 2014</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ma_2014/index.html">Introduction to Multiple Sequence Alignments, UPF, October 2014</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ug_2014/index.html">Introduction to Sequence Comparison, UPF, October 2014</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./bologna_ma_2014/index.html">RNA Analysis,Bologna,September 2014</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./uab_ma_2013/index.html">Sequence Comparison, UAB, November 2013</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./madrid_2013/index.html">Introduction to Pairwise 
-			      and Multiple Sequence Alignments, Madrid, November 2013</a></td>
-		      </tr>
-
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ug_2013/index.html">Introduction to Sequence Comparison, UPF, October 2013</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./bologna_ma_2013/index.html">RNA Analysis,Bologna,September 2013</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./vic_ma_2013/index.html">Sequence Comparison, VIC, March 2013</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./uab_ma_2012/index.html">Sequence Comparison, UAB, November 2012</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./madrid_2012/index.html">Introduction to Pairwise 
-			      and Multiple Sequence Alignments, Madrid, November 2012</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ma_2012/index.html">Introduction to Multiple Sequence Alignments, UPF, October 2012</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ug_2012/index.html">Introduction to Sequence Comparison, UPF, October 2012</a></td>
-		      </tr>
-
-
-		      <tr align=center>
-			<td><font size=+1><A HREF="./madrid_2011/index.html">Introduction to Pairwise 
-			      and Multiple Sequence Alignments, Madrid, November 2011</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ma_2011/index.html">Introduction to Multiple Sequence Alignments, UPF, October 2011</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ug_2011/index.html">Introduction to Sequence Comparison, UPF, October 2011</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./Bilbao_2011/index.html">Introduction to Multiple Sequence Alignments, Bilbao, July 2011</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./Tangier_EMBO_2011/index.html">Introduction to Protein Sequence Alignments (Multiple and Pairwise), EMBO Course, Tangier, June 2011</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./madrid_2010/index.html">Introduction to Pairwise 
-			      and Multiple Sequence Alignments, Madrid, November 2010</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ma_2010/index.html">Introduction to Multiple Sequence Alignments,UPF,October 2010</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./saragosa_pb_2010/index.html">Introduction to Multiple Sequence Alignments,Saragosa,April 2010</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ug_2010/index.html">Introduction to Sequence Comparison, UPF, January 2010</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./madrid_2009/index.html">Introduction to Pairwise and Multiple Sequence Alignments, Madrid, November 2009</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ma_2009/index.html">Introduction To Multiple Sequence Alignment,UPF, October 2009</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_ug_2009/index.html">Introduction to Sequence Comparison, UPF, January 2009</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./madrid_2008/index.html">Introduction to Pairwise and Multiple Sequence Alignments, Madrid, November 2008</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_2008/index.html">Introduction To Multiple Sequence Alignment,UPF, October 2008</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./upf_2007/index.html">Introduction To Multiple Sequence Alignment,UPF, November 2007</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./madrid_2007/index.html">Introduction To Multiple Sequence Alignment,Madrid, November 2007</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="./sardinia_07/index.html">Introduction To Sequence Analysis, Polaris (Italy), May 2007</a></td>
-		      </tr>
-		      <tr align=center>
-			<td><font size=+1><A HREF="../anonymous_sequence/index.html">An Anonymous Sequence for the Online Supplement of Bioinformatics For Dummies</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./pavie_07/index.html">Introduction To Perl, February 2007</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./bergin_06/index.html">Introduction To Sequence Analysis, Bergin (Norway), May 2006</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./sardinia_06/index.html">Introduction To Sequence Analysis, Polaris (Italy), May 2006</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./bgp_2001/index.html">Cell Biology, Lausanne (Switzerland), December 2001</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./sanbi_course_00/exercises.html">Sanbi, Johanesburg, Capetown (SA), November 1999</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./EmbnetCourse_99/problems.html">EMBnet, Lausanne (Switzerland), September 1999</a></td>
-		      </tr>
-		      
-		      <tr align=center>
-			<td><font size=+1><A HREF="./turkey_00/exercises.html">Introduction to bioinformatics (Exercises)</a></td>
-		      </tr>
-		      
-		      <tr align=center >
-			<td><font size=+1><A HREF="./Maln/index.html">Multiple Alignments (Course + Exercises)</a></td>
-		      </tr>
-		      
-		      <tr align=center >
-			<td><font size=+1><A HREF="./Aln/Perl_examples/aln_algorithms.html">Sequence Alignment Algorithms in Perl</a></td>
-		      </tr>
-		      
-		      <tr align=center >
-			<td><font size=+1><A HREF="./SEQ1/seq_list.html">Anonymous Sequences</a></td>
-		      </tr>
-		    </table>
-		    <BR><BR>
-			
-   <p><font size="2">Questions should be sent to <a href="mailto:cedric.notredame@europe.com">C.Notredame</a> </font></center>
-</center>
- </body>
- </html>
diff --git a/public_html/Courses/anonymous_sequence/index.html b/public_html/Courses/anonymous_sequence/index.html
index 15de80a..8672c9b 100755
--- a/public_html/Courses/anonymous_sequence/index.html
+++ b/public_html/Courses/anonymous_sequence/index.html
@@ -36,4 +36,4 @@
     <td>The home of bacterial genomes</td></tr>                              
 </table>
 <BR><BR>
-</table><p><a href=../../index.html>Return to The Main Page</a></p><p><font size="2">Questions should be sent to <a href="mailto:cedric.notredame@europe.com">cedric.notredame@europe.com</a> </font></center><table BGCOLOR=white Align=center width=70% Border=10><tr><td><center><p>This Entire Course Was Automatically Generated Using BED, the Bioinformatics Exercise Database. BED is a freeware available from <a href="cedric.notredame@europe.com">cedric.notredame@europe.com</a></p></center></td></tr></table><BR><BR> </body> </html>
\ No newline at end of file
+</table><p><a href=../../index.html>Return to The Main Page</a></p><p><font size="2">Questions should be sent to <a href="mailto:cedric.notredame@gmail.com">cedric.notredame@gmail.com</a> </font></center><table BGCOLOR=white Align=center width=70% Border=10><tr><td><center><p>This Entire Course Was Automatically Generated Using BED, the Bioinformatics Exercise Database. BED is a freeware available from <a href="cedric.notredame@gmail.com">cedric.notredame@gmail.com</a></p></center></td></tr></table><BR><BR> </body> </html>
diff --git a/public_html/Documentation/align_pdb.doc.txt b/public_html/Documentation/align_pdb.doc.txt
index ae9acd1..98afb06 100755
--- a/public_html/Documentation/align_pdb.doc.txt
+++ b/public_html/Documentation/align_pdb.doc.txt
@@ -398,7 +398,7 @@ B-Local Alignment (Lalign and SW)
 	13402 Marseille Cedex 20,
 	France
 
-	Email   :  cedric.notredame@europe.com
+	Email   :  cedric.notredame@gmail.com
 	WWW     :  http://igs-server.cnrs-mrs.fr/~cnotred/
 	Tel.    :  +33 491 164 606
 	Tel mob :  +33 661 312 531
diff --git a/public_html/Documentation/aln_compare.doc.txt b/public_html/Documentation/aln_compare.doc.txt
index d67d4c7..241383f 100755
--- a/public_html/Documentation/aln_compare.doc.txt
+++ b/public_html/Documentation/aln_compare.doc.txt
@@ -222,7 +222,7 @@ C.N.R.S UMR 1889
 13402 Marseille Cedex 20,
 France
 
-Email   :  cedric.notredame@europe.com
+Email   :  cedric.notredame@gmail.com
 WWW     :  http://igs-server.cnrs-mrs.fr/~cnotred/
 Tel.    :  +33 491 164 606
 Tel mob :  +33 661 312 531
diff --git a/public_html/Documentation/analyse_pdb.doc.txt b/public_html/Documentation/analyse_pdb.doc.txt
index 67a2be2..77c7dd1 100755
--- a/public_html/Documentation/analyse_pdb.doc.txt
+++ b/public_html/Documentation/analyse_pdb.doc.txt
@@ -292,6 +292,6 @@ specific parameters.
 7-BUG REPORTS
       please report all bugs and problems to:
 
-	    cedric.notredame@europe.com
+	    cedric.notredame@gmail.com
  	  
 	
diff --git a/public_html/Projects/blastr/index.html b/public_html/Projects/blastr/index.html
index 0324b29..3349a18 100755
--- a/public_html/Projects/blastr/index.html
+++ b/public_html/Projects/blastr/index.html
@@ -347,7 +347,7 @@
 
 				  Spain                                      <br>
 
-				  Email:  <a href="mailto:cedric.notredame@europe.com">cedric.notredame@europe.com</a>
+				  Email:  <a href="mailto:cedric.notredame@gmail.com">cedric.notredame@gmail.com</a>
     <br>
 
 				  HOME :  <a href="http://www.tcoffee.org/homepage.html">http://www.tcoffee.org/homepage.html</a><br>
diff --git a/public_html/Projects/expresso/index.html b/public_html/Projects/expresso/index.html
index 73eedc1..c1f9a6b 100755
--- a/public_html/Projects/expresso/index.html
+++ b/public_html/Projects/expresso/index.html
@@ -262,7 +262,7 @@
 				  Dr Aiguader, 88                            <br>
 				  08003 Barcelona                            <br>
 				  Spain                                      <br>
-				  Email:  <A href="MAILTO:cedric.notredame@europe.com">cedric.notredame@europe.com</A>    <br>
+				  Email:  <A href="MAILTO:cedric.notredame@gmail.com">cedric.notredame@gmail.com</A>    <br>
 				  HOME :  <A HREF="http://www.tcoffee.org/index.html">http://www.tcoffee.org/</A><br>
 				  GROUP:  <a href="http://pasteur.crg.es/portal/page/portal/Internet/02_Research/01_Programmes/01_Bioinformatics_Genomics/03_Comparative_Bioinformatics">CRG</A><br>
 				  Phone:  +34 933 160 271                <br>
diff --git a/public_html/Projects/mcoffee/index.html b/public_html/Projects/mcoffee/index.html
index e55054d..1ce7804 100755
--- a/public_html/Projects/mcoffee/index.html
+++ b/public_html/Projects/mcoffee/index.html
@@ -242,7 +242,7 @@
 				  Dr Aiguader, 88                            <br>
 				  08003 Barcelona                            <br>
 				  Spain                                      <br>
-				  Email:  <A href="MAILTO:cedric.notredame@europe.com">cedric.notredame@europe.com</A>    <br>
+				  Email:  <A href="MAILTO:cedric.notredame@gmail.com">cedric.notredame@gmail.com</A>    <br>
 				  HOME :  <A HREF="http://www.tcoffee.org/">http://www.tcoffee.org/</A><br>
 				  GROUP:  <a href="http://pasteur.crg.es/portal/page/portal/Internet/02_Research/01_Programmes/01_Bioinformatics_Genomics/03_Comparative_Bioinformatics">CRG</A><br>
 				  Phone:  +34 933 160 271                <br>
diff --git a/public_html/Projects/mocca/index.html b/public_html/Projects/mocca/index.html
index 1e2c2d4..372d795 100755
--- a/public_html/Projects/mocca/index.html
+++ b/public_html/Projects/mocca/index.html
@@ -66,14 +66,14 @@ <H2 align=center><font color=red>Multiple OCCurences analysis</font></H2>
 	      There is currently no mocca server up and running but I will
 	      be happy to help setting one up.
 	      If you wish to create a mocca server, please inform <A
-	      HREF="mailto:cedric.notredame@europe.com">me</A> and I will link
+	      HREF="mailto:cedric.notredame@gmail.com">me</A> and I will link
 	      your server to this page. 
               </P>	
 	      			
 <LI><H2><FONT COLOR="#8B4513">Bug Reports and mailing list</FONT></H2> </LI>			    
 <P>Mocca is a new method and feed back is very important. If
 appropriate, a mailing list will be maintained here. Please send me an
-Email if you wish to make a request or a comment <A HREF="mailto:cedric.notredame@europe.com">cedric.notredame@europe.com</A></P>
+Email if you wish to make a request or a comment <A HREF="mailto:cedric.notredame@gmail.com">cedric.notredame@gmail.com</A></P>
 </UL>	
 </BODY>
 </HTML>
diff --git a/public_html/Projects/procoffee/index.html b/public_html/Projects/procoffee/index.html
index a888101..23af7c3 100755
--- a/public_html/Projects/procoffee/index.html
+++ b/public_html/Projects/procoffee/index.html
@@ -246,7 +246,7 @@
 				  Dr Aiguader, 88                            <br>
 				  08003 Barcelona                            <br>
 				  Spain                                      <br>
-				  Email:  <a href="mailto:cedric.notredame@europe.com">cedric.notredame@europe.com</a>    <br>
+				  Email:  <a href="mailto:cedric.notredame@gmail.com">cedric.notredame@gmail.com</a>    <br>
 				  HOME :  <a href="http://www.tcoffee.org/homepage.html">http://www.tcoffee.org/homepage.html</a><br>
 				  GROUP:  <a href="http://pasteur.crg.es/portal/page/portal/Internet/02_Research/01_Programmes/01_Bioinformatics_Genomics/03_Comparative_Bioinformatics">CRG</a><br>
 				  Phone:  +34 933 160 271                <br>
diff --git a/public_html/Projects/procoffee/procoffee_home_page_old.html b/public_html/Projects/procoffee/procoffee_home_page_old.html
index 09f8b04..4e8cce0 100755
--- a/public_html/Projects/procoffee/procoffee_home_page_old.html
+++ b/public_html/Projects/procoffee/procoffee_home_page_old.html
@@ -241,7 +241,7 @@
 				  Dr Aiguader, 88                            <br>
 				  08003 Barcelona                            <br>
 				  Spain                                      <br>
-				  Email:  <a href="mailto:cedric.notredame@europe.com">cedric.notredame@europe.com</a>    <br>
+				  Email:  <a href="mailto:cedric.notredame@gmail.com">cedric.notredame@gmail.com</a>    <br>
 				  HOME :  <a href="http://www.tcoffee.org/homepage.html">http://www.tcoffee.org/homepage.html</a><br>
 				  GROUP:  <a href="http://pasteur.crg.es/portal/page/portal/Internet/02_Research/01_Programmes/01_Bioinformatics_Genomics/03_Comparative_Bioinformatics">CRG</a><br>
 				  Phone:  +34 933 160 271                <br>
diff --git a/public_html/Projects/rcoffee/index.html b/public_html/Projects/rcoffee/index.html
index 04a56e1..db663ba 100755
--- a/public_html/Projects/rcoffee/index.html
+++ b/public_html/Projects/rcoffee/index.html
@@ -47,7 +47,7 @@ <H2 align=center><font color=red>Multiple RNA Sequence Alignments</font></H2>
     <UL>
 	<P>
       <LI>Please download the latest T-Coffee version and its documentation <A HREF="../tcoffee/index.html">T-Coffee Home page</A></LI>
-      <LI>Previous versions are available on request: <A HREF="mailto:cedric.notredame@europe.com">cedric.notredame@europe.com</A></LI>
+      <LI>Previous versions are available on request: <A HREF="mailto:cedric.notredame@gmail.com">cedric.notredame@gmail.com</A></LI>
       <LI>To make the best of R-Coffee you will also need to install the following packages:
 	<BR><BR><UL>
 	  <LI>RNAlpfold frorm the vienna package (<b>Compulsory</b>) [<A HREF="http://www.tbi.univie.ac.at/~ivo/RNA/">*</A>]</LI>
diff --git a/public_html/Projects/robusta/index.html b/public_html/Projects/robusta/index.html
index a3422f2..f96e1ac 100644
--- a/public_html/Projects/robusta/index.html
+++ b/public_html/Projects/robusta/index.html
@@ -243,7 +243,7 @@
 				  Dr Aiguader, 88                            <br>
 				  08003 Barcelona                            <br>
 				  Spain                                      <br>
-				  Email:  <A href="MAILTO:cedric.notredame@europe.com">cedric.notredame@europe.com</A>    <br>
+				  Email:  <A href="MAILTO:cedric.notredame@gmail.com">cedric.notredame@gmail.com</A>    <br>
 				  HOME :  <A HREF="http://www.tcoffee.org/homepage.html">http://www.tcoffee.org/homepage.html</A><br>
 				  GROUP:  <a href="http://pasteur.crg.es/portal/page/portal/Internet/02_Research/01_Programmes/01_Bioinformatics_Genomics/03_Comparative_Bioinformatics">CRG</A><br>
 				  Phone:  +34 933 160 271                <br>
diff --git a/public_html/Projects/robusta/index.html~ b/public_html/Projects/robusta/index.html~
deleted file mode 100644
index c3cf06e..0000000
--- a/public_html/Projects/robusta/index.html~
+++ /dev/null
@@ -1,293 +0,0 @@
- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html>
-  <head>
-
-    <title>Robusta Home Page</title>
-
-<!-- Google tag (gtag.js) -->
-<script async src="https://www.googletagmanager.com/gtag/js?id=G-W0ZCV3Q3DG"></script>
-<script>
-  window.dataLayer = window.dataLayer || [];
-  function gtag(){dataLayer.push(arguments);}
-  gtag('js', new Date());
-
-  gtag('config', 'G-W0ZCV3Q3DG');
-</script>
-
-  </head>
-    <BODY TEXT="#000000" BGCOLOR=white LINK="#0000EE" VLINK="#551A8B" ALINK="#FF0000">
-    <FONT FACE="Arial">
-    <center>
-
- <table width="80%"       cellpadding=15 cellspacing=0 bgcolor="#FFEBCD" border=1 bordercolor="#8B4513">
-	  <tr>
-	    <td>
-	      <table width="100%" cellpadding=15 cellspacing=0 cellborder=0 valign="TOP" border=0>
-		  <tr bgcolor="#FFEBCD" >
-		    <td colspan=1 bgcolor="#FFEBCD" width="5%"><br></td>
-		    <td colspan=1 bgcolor="#FFEBCD" width="40%"><br></td>
-		    <td colspan=1 bgcolor="#FFEBCD" width="5%"><br></td>
-		    <td colspan=1 bgcolor="#FFEBCD" width="40%"><br></td>
-		    <td colspan=1 bgcolor="#FFEBCD" width="5%"><br></td>
-		  </tr>
-
-		  <tr>
-		    <td colspan=5 bgcolor="#FFEBCD">
-		      <center><table><tr><td align="center"><b> <FONT size="7" color="#8B4513">Robusta <br>A Meta-Multiple Genome Alignment Tool</font></b></td></tr></table></center>
-		    </td>
-		  </tr>
-
-		  <tr>
-		    <td colspan=5 bgcolor="#FFEBCD"><br></td>
-		  </tr>
-
-
-		  <tr>
-		    <td colspan=5 bgcolor="#FFE4C4">
-		      <HR>
-		      <center>
-			<table width="100%" cellpadding=15 cellspacing=0 cellborder=0 valign=top>
-			    <tr align=center>
-			      <td width="15%" onMouseOver="style.backgroundColor='white';"onmouseout="style.backgroundColor='#FFE4C4'"><b><a href="../homepage.html"><font color="#8B4513">HOME</font></a></b></td>
-			      <td width="15%" onMouseOver="style.backgroundColor='white';"onmouseout="style.backgroundColor='#FFE4C4'"><b><a href="#SERVERS"><font color="#8B4513">SERVERS</font></a></b></td>
-			      <td width="15%" onMouseOver="style.backgroundColor='white';"onmouseout="style.backgroundColor='#FFE4C4'"><b><a href="#DOWNLOAD"><font color="#8B4513">DOWNLOAD</font></a></b></td>
-			      <td width="15%" onMouseOver="style.backgroundColor='white';"onmouseout="style.backgroundColor='#FFE4C4'"><b><a href="#COMMANDS"><font color="#8B4513">DOCUMENTATION</font></a></b></td>
-			      <td width="15%" onMouseOver="style.backgroundColor='white';"onmouseout="style.backgroundColor='#FFE4C4'"><b><a href="#OUTPUT"><font color="#8B4513">OUTPUT</font></a></b></td>
-			      <td width="15%" onMouseOver="style.backgroundColor='white';"onmouseout="style.backgroundColor='#FFE4C4'"><b><a href="#CONTACT"><font color="#8B4513">CONTACT</font></a></b></td>
-
-			    </tr>
-
-			</table>
-		      </center>
-		      <HR>
-		    </td>
-		  </tr>
-
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-		    <td colspan=5 bgcolor="#FFEBCD"><br></td>
-		  </tr>
-
-		  <tr>
-		    <td rowspan=3 bgcolor="#FFEBCD"><br></td>
-		    <td rowspan=3 bgcolor="white" valign="top">
-		      <center><h2><FONT color="#8B4513">What is Robusta?</FONT></h2></center>
-		      <table bgcolor="white">
-			  <tr>
-			    <td>
-			      <P align="justify">
-			      Robusta is a meta multiple genome alignment package. It does not produce any alignment by itself but can combine alignments of different genome alignment programs into a single final alignment. It is able to call serveral different pairwise and multiple genome alignment programs. The results of these programs are parsed and turned into a T-Coffee library. Using T-Coffee the alignments are then turned into the final alignment.
-			      Currently two pairwise genome aligner and three multiple genome alignment programs are included into this framework.
-			      A typical usage would be to cut the genomes to align into a set of collinear homologous blocks using Mercator. These blocks are than aligned and turned into libraries using Robusta. As a final step T-Coffee is called to produce an alignment for each block.
-			    </td>
-			  </tr>
-		      </table>
-
-		    </td>
-
-		    <td colspan=1 rowspan=3 bgcolor="#FFEBCD"><br></td>
-		    <td colspan=1 rowspan=1 bgcolor="white">
-		      <center><h2><FONT color="#8B4513"><a name="SERVERS">SERVERS</a></font></h2></center>
-		      <table bgcolor="white">
-
-			  <tr><td>
-			      <UL>
-				<LI><A HREF="http://www.tcoffee.org">www.tcoffee.org</A></LI>
-			      </UL>
-			    </td></tr>
-		      </table>
-		    <td rowspan=3 bgcolor="#FFEBCD"><br></td>
-		  </tr>
-
-		  <tr>
-		    <td bgcolor="#FFEBCD"><br></td>
-		  </tr>
-
-		  <tr>
-		    <td colspan=1 rowspan=1 bgcolor="white">
-		      <center><h2><FONT color="#8B4513"><a name="DOWNLOAD">DOWNLOAD</a></font></h2></center>
-		      <table bgcolor="white">
-			  <tr><td>
-			      <UL>
-				<LI>Robusta is a seperate program for the Linux operating system and needs several programs to be installed: T-Coffee to combine the libraries and one or serveral genome alignment programs.</LI>
-			      <li><a href="robusta" >Click here to download Robusta binary</a></li>
-			      </UL>
-			      
-			    </td></tr>
-		      </table>
-		    </td>
-		  </tr>
-
-		  <tr>
-		    <td colspan=5 bgcolor="#FFEBCD"><br></td>
-		  </tr>
-		  <tr>
-		    <td bgcolor="#FFEBCD"><br></td>
-		    <td colspan=3 bgcolor="white" valign="top">
-		      <center><h2><FONT color="#8B4513"><a name="INSTALLATION">INSTALLATION</a></font></h2></center>
-		      <table bgcolor="white">
-			  <tr>
-			    <td>
-			      <P align="justify"><b>1-</b>Download the executable or use Git to get the source code of the current version: "git clone https://github.com/cbcrg/robusta.git"</P>
-			    </td>
-			  </tr>
-			  <tr>
-			    <td>
-			      <P align="justify"><b>2-</b> If you downloaded the source code change into the g_coffee directory and type "make mode=release". </P>
-			    </td>
-			  </tr>
-			  <tr>
-
-			  </tr>
-		      </table>
-		    </td>
-		    <td bgcolor="#FFEBCD"><br></td>
-		  </tr>
-
-		  <tr>
-		    <td colspan=5 bgcolor="#FFEBCD"><br></td>
-		  </tr>
-		  <tr>
-		    <td colspan=1 rowspan=5 bgcolor="#FFEBCD"><br></td>
-		    <td colspan=1 rowspan=5 bgcolor="white" valign="top">
-		      <center><h2><FONT color="#8B4513"><a name="OUTPUT">OUTPUT</a></font></h2></center>
-		      <center><table bgcolor="white">
-			    <tr>
-			      <td>
-				<P align=justify>Given a sequence file <code>foo.pep</code> Robusta produces a library which can be turned into an alignment using T-Coffee. See below for a small benchmark using different combinations of genome alignment programs. <br>
-				9 Rickettsia genomes were first seperated into blocks using Mectator and than aligned using Robusta with different alignments. All Robusta Variants are starting with G.
-				</P>
-				<img border="0" src="g_coffee_rickettsia_9_conservation.jpeg">
-			      </td>
-			    </tr>
-			</table></center>
-		    </td>
-		    <td colspan=1 rowspan=5 bgcolor="#FFEBCD"><br></td>
-		    <td colspan=1 bgcolor="white" valign="top">
-		      <center><h2><FONT color="#8B4513"><a name="COMMANDS">DOCUMENTATION</a></font></h2></center>
-		      <table bgcolor="white">
-			  <tr>
-			    <td>
-			      <p>The full documentation is on the <a href="../tcoffee/index.html#DOCUMENTATION">T-Coffee Homepage</a>. But the following shortcuts may be useful.</p>
-			      <TABLE border=0 WIDTH="100%" CELLPADDING="5" bgcolor="white">
-				  <tr>
-				    <TD bgcolor="grey"></td>
-				  </tr>
-				  <TR>
-				    <TD>To run Robusta using lastz and cgaln, type</td>
-				  </TR>
-				  <tr>
-				    <td>
-				      <code>g_coffee -i <i>foo.seq</i> -p lastz,cgaln -o <i>foo.lib</i> </code><br />
-				      And then use T-Coffee to produce the final alignment:<br />
-				      <code>t_coffee -lib <i>foo.lib</i> </code>
-				    </td>
-				  </TR>
-				  <tr>
-				    <TD bgcolor="grey"></td>
-				  </tr>
-				  <TR>
-				    <TD>For an overview of all options type: </td>
-				  </TR>
-				  <tr>
-				    <td>
-				      <code>g_coffe -h </code>
-				    </td>
-				  </TR>
-				  <tr>
-				    <TD colspan=3 bgcolor="grey"></td>
-				  </tr>
-			      </table>
-
-			    </td>
-			  </tr>
-		      </table>
-		    </td>
-		    <td colspan=1 rowspan=5 bgcolor="#FFEBCD"><br></td>
-		  </tr>
-		  <tr>
-		    <td colspan=1 bgcolor="#FFEBCD"><br></td>
-		  </tr>
-
-		  <tr>
-		    <td bgcolor="white" valign="top">
-		      <center><h2><FONT color="#8B4513"><a name="LINKS">LINKS</a></font></h2></center>
-		      <table bgcolor="white">
-			  <tr>
-			    <td>
-			      <LI><A HREF="../../Resources/aligner_list.html">MSA Mehods</A> Available for combination within M-Coffee</LI>
-			    </td>
-			  </tr>
-		      </table>
-		    </td>
-		  </tr>
-
-		  <tr>
-		    <td colspan=1 bgcolor="#FFEBCD"><br></td>
-		  </tr>
-		  <tr>
-		    <td bgcolor="white" valign="top">
-		      <center><h2><FONT color="#8B4513"><a name="CONTACT">CONTACT</a></font></h2></center>
-		      <table bgcolor="white">
-			  <tr>
-			    <td>
-			      <P>Our projects relie on your feeback. Please send me an
-				E-mail if you wish to make a request, a comment, or report a bug!
-				<code>
-				  <br><br>
-				  *******************************************<br>
-				  Dr. Cedric Notredame, PhD.                 <br>
-				  Group Leader                               <br>
-				  Comparative Bioinformatics Group           <br>
-				  Bioinformatics and Genomics Programme      <br>
-				  Center for Genomic Regulation (CRG)        <br>
-				  Dr Aiguader, 88                            <br>
-				  08003 Barcelona                            <br>
-				  Spain                                      <br>
-				  Email:  <A href="MAILTO:cedric.notredame@europe.com">cedric.notredame@europe.com</A>    <br>
-				  HOME :  <A HREF="http://www.tcoffee.org/homepage.html">http://www.tcoffee.org/homepage.html</A><br>
-				  GROUP:  <a href="http://pasteur.crg.es/portal/page/portal/Internet/02_Research/01_Programmes/01_Bioinformatics_Genomics/03_Comparative_Bioinformatics">CRG</A><br>
-				  Phone:  +34 933 160 271                <br>
-				  *******************************************       <br>
-				</code>
-			    </td>
-			  </tr>
-		      </table>
-		    </td>
-		  </tr>
-
-		  <tr>
-		    <td colspan=5 bgcolor="#FFEBCD"><br></td>
-		  </tr>
-
-		  <tr>
-		    <td colspan=5 bgcolor="#FFE4C4">
-
-		      <center>
-			<HR>
-				<table width="100%" cellpadding=15 cellspacing=0 cellborder=0 valign=top>
-			    <tr align=center>
-			      <td width="15%" onMouseOver="style.backgroundColor='white';"onmouseout="style.backgroundColor='#FFE4C4'"><b><a href="../homepage.html"><font color="#8B4513">HOME</font></a></b></td>
-			      <td width="15%" onMouseOver="style.backgroundColor='white';"onmouseout="style.backgroundColor='#FFE4C4'"><b><a href="#SERVERS"><font color="#8B4513">SERVERS</font></a></b></td>
-			      <td width="15%" onMouseOver="style.backgroundColor='white';"onmouseout="style.backgroundColor='#FFE4C4'"><b><a href="#DOWNLOAD"><font color="#8B4513">DOWNLOAD</font></a></b></td>
-			      <td width="15%" onMouseOver="style.backgroundColor='white';"onmouseout="style.backgroundColor='#FFE4C4'"><b><a href="#COMMANDS"><font color="#8B4513">DOCUMENTATION</font></a></b></td>
-			      <td width="15%" onMouseOver="style.backgroundColor='white';"onmouseout="style.backgroundColor='#FFE4C4'"><b><a href="#OUTPUT"><font color="#8B4513">OUTPUT</font></a></b></td>
-			      <td width="15%" onMouseOver="style.backgroundColor='white';"onmouseout="style.backgroundColor='#FFE4C4'"><b><a href="#CONTACT"><font color="#8B4513">CONTACT</font></a></b></td>
-
-			    </tr>
-
-			</table>
-			<HR>
-		      </center>
-
-		    </td>
-    </center>
-  </td>
-  </tr>
-  </table>
-  </td>
-  </tr>
-  </table>
-  </center>
-  </font>
-  </body>
-</html>
diff --git a/public_html/Projects/saracoffee/index.html b/public_html/Projects/saracoffee/index.html
index 441f150..0bb862a 100644
--- a/public_html/Projects/saracoffee/index.html
+++ b/public_html/Projects/saracoffee/index.html
@@ -322,7 +322,7 @@
 
 				  Spain                                      <br>
 
-				  Email:  <a href="mailto:cedric.notredame@europe.com">cedric.notredame@europe.com</a>
+				  Email:  <a href="mailto:cedric.notredame@gmail.com">cedric.notredame@gmail.com</a>
     <br>
 
 				  HOME :  <a href="http://www.tcoffee.org/homepage.html">http://www.tcoffee.org/homepage.html</a><br>
diff --git a/public_html/Projects/strike/index (palestine.crg.es's conflicted copy 2016-05-05).html b/public_html/Projects/strike/index (palestine.crg.es's conflicted copy 2016-05-05).html
deleted file mode 100755
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@@ -1,381 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html><head>
-<meta http-equiv="content-type" content="text/html; charset=utf-8">
-    <title> STRIKE Home Page</title>
-  </head><body link="#0000ee" text="#000000" vlink="#551a8b"
-alink="#ff0000" bgcolor="white">
-    <font face="Arial">
-    </font><center>
-<font face="Arial">
- <table width="80%" bgcolor="#ffebcd" border="1" bordercolor="#8b4513"
-cellpadding="15" cellspacing="0">
-	  <tbody><tr>
-	    <td>
-
-	      <table cellborder="0" valign="TOP" width="100%" border="0"
-cellpadding="15" cellspacing="0">
-		  <tbody><tr bgcolor="#ffebcd">
-		    <td colspan="1" width="5%" bgcolor="#ffebcd"><br></td>
-		    <td colspan="1" width="40%" bgcolor="#ffebcd"><br></td>
-		    <td colspan="1" width="5%" bgcolor="#ffebcd"><br></td>
-		    <td colspan="1" width="40%" bgcolor="#ffebcd"><br></td>
-		    <td colspan="1" width="5%" bgcolor="#ffebcd"><br></td>
-		  </tr>
-
-
-		  <tr>
-
-		    <td colspan="5" bgcolor="#ffebcd">
-		      <center><table><tbody><tr><td align="center"><b> <font
-color="#8b4513" size="7">STRIKE <br>A sequence alignment scoring tool</font></b></td></tr></tbody></table></center>
-		    </td>
-		  </tr>
-
-		  <tr>
-
-		    <td colspan="5" bgcolor="#ffebcd"><br></td>
-
-		  </tr>
-
-
-
-		  <tr>
-		    <td colspan="5" bgcolor="#ffe4c4">
-		      <hr>
-		      <center>
-			<table cellborder="0" valign="top" width="100%" cellpadding="15"
-cellspacing="0">
-
-			    <tbody><tr align="center">
-
-			      <td onmouseover="style.backgroundColor='white';"
-onmouseout="style.backgroundColor='#FFE4C4'" width="15%"><b><a
-href="http://www.tcoffee.org/homepage.html"><font color="#8b4513">HOME</font></a></b></td>
-
-			      <td onmouseover="style.backgroundColor='white';"
-onmouseout="style.backgroundColor='#FFE4C4'" width="15%"><b><a
-href="#SERVERS"><font color="#8b4513">SERVERS</font></a></b></td>
-
-			      <td style="background-color: rgb(255, 228, 196);"
-onmouseover="style.backgroundColor='white';"
-onmouseout="style.backgroundColor='#FFE4C4'" width="15%"><b><a
-href="#DOWNLOAD"><font color="#8b4513">DOWNLOAD</font></a></b></td>
-			      <td style="background-color: rgb(255, 228, 196);"
-onmouseover="style.backgroundColor='white';"
-onmouseout="style.backgroundColor='#FFE4C4'" width="15%"><b><a
-href="#COMMANDS"><font color="#8b4513">DOCUMENTATION</font></a></b></td>
-
-
-			      <td onmouseover="style.backgroundColor='white';"
-onmouseout="style.backgroundColor='#FFE4C4'" width="15%"><b><a
-href="#CONTACT"><font color="#8b4513">CONTACT</font></a></b></td>
-
-
-			    </tr>
-
-
-			</tbody></table>
-		      </center>
-
-		      <hr>
-		    </td>
-
-		  </tr>
-
-		  <tr>
-		    <td colspan="5" bgcolor="#ffebcd"><br></td>
-
-		  </tr>
-
-
-		  <tr>
-		    <td rowspan="3" bgcolor="#ffebcd"><br></td>
-		    <td rowspan="1" valign="top" bgcolor="white">
-
-		      <center><h2><font color="#8b4513">What is STRIKE?</font></h2></center>
-		      <table bgcolor="white">
-			  <tbody><tr>
-
-			    <td>
-			      <p align="justify">
-STRIKE (Single sTRucture Induced Evaluation) is a program to evaluate protein multiple sequence alignments using a single protein structure.
-</p>
-			      <!-- MAYBE .. ;) <p>A list of related publications is available <a href="http:">here</a> -->
-			    </td>
-
-			  </tr>
-		      </tbody></table>
-
-		    </td>
-
-
-		    <td colspan="1" rowspan="3" bgcolor="#ffebcd"><br></td>
-		    <td colspan="1" rowspan="1" bgcolor="white">
-
-		      <center><h2><font color="#8b4513"><a name="DOWNLOAD">DOWNLOAD</a></font></h2></center>
-		      <table bgcolor="white">
-			  <tbody><tr><td>
-
-			      <ul>
-				<li><b>Download the package <a target="_blank" href="./strike_v1.2.tar.bz2" target="_blank">here</a></b>
-			    </td></tr>
-
-		      </tbody></table>
-
-		    </td><td rowspan="3" bgcolor="#ffebcd"><br></td>
-		  </tr>
-
-		  <tr>
-		    <td bgcolor="#ffebcd"><br></td>
-
-		  </tr>
-
-		  <tr>
-		    <td colspan="1" rowspan="1" bgcolor="#ffebcd">
-
-		    </td>
-
-		  </tr>
-
-		  <tr>
-		    <td colspan="5" bgcolor="#ffebcd"><br></td>
-		  </tr>
-		  <tr>
-
-		    <td bgcolor="#ffebcd"><br></td>
-
-		    <td colspan="3" valign="top" bgcolor="white">
-
-		      <center><h2><font color="#8b4513"><a name="INSTALLATION">INSTALLATION</a></font></h2></center>
-
-		      <table bgcolor="white">
-			  <tbody><tr>
-			    <td>
-			      <p align="justify">
-
-
-Typing 'make' in the command line will produce the executable.
-			      </p>
-
-			    </td>
-			  </tr>
-			  <tr>
-			    </tr><tr><td><br></td></tr>
-			    <tr><td>
-			    </p></td>
-			  </tr>
-		      </tbody></table>
-
-		    </td>
-
-		    <td bgcolor="#ffebcd"><br></td>
-		  </tr>
-
-		  <tr>
-		    <td colspan="5" bgcolor="#ffebcd"><br></td>
-		  </tr>
-		  <tr>
-		    <td colspan="1" rowspan="5" bgcolor="#ffebcd"><br></td>
-
-		    <td colspan="1" rowspan="5" valign="top" bgcolor="white">
-		      <center><h2><font color="#8b4513">The Program</font></h2></center>
-
-		      <center><table bgcolor="white">
-			    <tbody><tr>
-			      <td>
-				<p align="justify">
-		STRIKE uses the STRIKE matrix to evaluate an alignment. This matrix gives a score for a contact similar to the Blosum matrix which gives a score to each nucleotide match. Contacts from the given structure are projected onto the alignment and each projected contact is scored.
-
-		The result is a single score for the whole alignment. The higher the score, the better is the agreement between alignmetn and structure.
-</p>
-			      </td>
-
-			    </tr>
-			</tbody></table></center>
-		    </td>
-
-		    <td colspan="1" rowspan="5" bgcolor="#ffebcd"><br></td>
-
-		    <td colspan="1" valign="top" bgcolor="white">
-
-		      <center><h2><font color="#8b4513"><a name="COMMANDS">DOCUMENTATION</a></font></h2></center>
-		      <table bgcolor="white">
-			  <tbody><tr>
-
-			    <td>
-			      <p> A detailed description is given in the incorporated Readme. The basic command is the following one:</p>
-
-			      <table width="100%" bgcolor="white" border="0" cellpadding="5">
-
-				  <tbody>
-
-<table bgcolor="white" border="0" cellpadding="5" width="100%">
-				  <tbody><tr>
-				    <td bgcolor="grey"></td>
-				  </tr>
-
-				  <tr>
-				    <td>Compute the score of an alignment:</td>
-
-				  </tr>
-
-				  <tr>
-				    <td>
-				       <code>  strike -c &lt;<i>template_file</i>&gt; -a  &lt;<i>alignment_file</i>&gt; </code>
-
-				    </td>
-
-				  </tr>
-				  <tr>
-
-				    <td bgcolor="grey"></td>
-</tr>
-
-
-
-
-
-			      </tbody></table>
-
-
-			    </td>
-
-			  </tr>
-		      </tbody></table>
-		    </td>
-		    <td colspan="1" rowspan="5" bgcolor="#ffebcd"><br></td>
-		  </tr>
-
-		  <tr>
-		    <td colspan="1" bgcolor="#ffebcd"><br></td>
-
-		  </tr>
-
-		  <tr>
-
-		    <td valign="top" bgcolor="white">
-<!-- 		      <center><h2><font color="#8b4513"><a name="LINKS"  >LINKS</a></font></h2></center> -->
-		      <table bgcolor="white">
-
-			  <tbody><tr>
-
-			    <td>
-
-<!-- 			      <li><a href="http://rfam.sanger.ac.uk/" target="_blank">Rfam</a></li> -->
-<!-- <li><a href="http://infernal.janelia.org/" target="_blank">Infernal</a></li> -->
-<!-- <li><a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi" target="_blank">NCBI-Blast</a></li> -->
-
-<!-- <li><a href="http://www.advbiocomp.com/blast.html" target="_blank">AB-Blast</a></li> -->
-
-			    </td>
-
-			  </tr>
-		      </tbody></table>
-
-		    </td>
-		  </tr>
-
-		  <tr>
-		    <td colspan="1" bgcolor="#ffebcd"><br></td>
-		  </tr>
-
-		  <tr>
-
-		    <td valign="top" bgcolor="white">
-		      <center><h2><font color="#8b4513"><a name="CONTACT">CONTACT</a></font></h2></center>
-
-		      <table bgcolor="white">
-			  <tbody><tr>
-			    <td>
-			      <p>Our projects rely on your feeback. Please send me an
-				E-mail if you wish to make a request, a comment, or report a bug!
-				<code>
-				  <br><br>
-
-				  *******************************************<br>
-				  Dr. Cedric Notredame, PhD.                 <br>
-				  Group Leader                               <br>
-
-				  Comparative Bioinformatics Group           <br>
-				  Bioinformatics and Genomics Programme      <br>
-				  Center for Genomic Regulation (CRG)        <br>
-
-				  Dr Aiguader, 88                            <br>
-				  08003 Barcelona                            <br>
-
-				  Spain                                      <br>
-
-				  Email:  <a href="mailto:cedric.notredame@europe.com">cedric.notredame@europe.com</a>
-    <br>
-
-				  HOME :  <a href="http://www.tcoffee.org/homepage.html">http://www.tcoffee.org/homepage.html</a><br>
-
-				  GROUP:  <a
-href="http://pasteur.crg.es/portal/page/portal/Internet/02_Research/01_Programmes/01_Bioinformatics_Genomics/03_Comparative_Bioinformatics">CRG</a><br>
-
-				  Phone:  +34 933 160 271                <br>
-
-				  *******************************************       <br>
-
-				</code>
-			    </p></td>
-			  </tr>
-		      </tbody></table>
-
-		    </td>
-
-		  </tr>
-
-		  <tr>
-
-		    <td colspan="5" bgcolor="#ffebcd"><br></td>
-		  </tr>
-
-		  <tr>
-		    <td colspan="5" bgcolor="#ffe4c4">
-		      <center>
-			<hr>
-
-				<table cellborder="0" valign="top" width="100%" cellpadding="15"
-cellspacing="0">
-			    <tbody><tr align="center">
-
-			      <td style="background-color: rgb(255, 228, 196);"
-onmouseover="style.backgroundColor='white';"
-onmouseout="style.backgroundColor='#FFE4C4'" width="15%"><b><a
-href="http://www.tcoffee.org/homepage.html"><font color="#8b4513">HOME</font></a></b></td>
-			      <td style="background-color: rgb(255, 228, 196);"
-onmouseover="style.backgroundColor='white';"
-onmouseout="style.backgroundColor='#FFE4C4'" width="15%"><b><a
-href="#SERVERS"><font color="#8b4513">SERVERS</font></a></b></td>
-			      <td style="background-color: rgb(255, 228, 196);"
-onmouseover="style.backgroundColor='white';"
-onmouseout="style.backgroundColor='#FFE4C4'" width="15%"><b><a
-href="#DOWNLOAD"><font color="#8b4513">DOWNLOAD</font></a></b></td>
-			      <td style="background-color: rgb(255, 228, 196);"
-onmouseover="style.backgroundColor='white';"
-onmouseout="style.backgroundColor='#FFE4C4'" width="15%"><b><a
-href="#COMMANDS"><font color="#8b4513">DOCUMENTATION</font></a></b></td>
-
-
-			      <td onmouseover="style.backgroundColor='white';"
-onmouseout="style.backgroundColor='#FFE4C4'" width="15%"><b><a
-href="#CONTACT"><font color="#8b4513">CONTACT</font></a></b></td>
-
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-
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-			<hr>
-		      </center>
-		    </td>
-  </tr>
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-  </font></center>
-<font face="Arial">  </font>
-  </body></html>
diff --git a/public_html/Projects/strike/index.html b/public_html/Projects/strike/index.html
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--- a/public_html/Projects/strike/index.html
+++ b/public_html/Projects/strike/index.html
@@ -305,7 +305,7 @@
 
 				  Spain                                      <br>
 
-				  Email:  <a href="mailto:cedric.notredame@europe.com">cedric.notredame@europe.com</a>
+				  Email:  <a href="mailto:cedric.notredame@gmail.com">cedric.notredame@gmail.com</a>
     <br>
 
 				  HOME :  <a href="http://www.tcoffee.org/homepage.html">http://www.tcoffee.org/homepage.html</a><br>
diff --git a/public_html/Projects/strike/index.html~ b/public_html/Projects/strike/index.html~
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-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html><head>
-<meta http-equiv="content-type" content="text/html; charset=utf-8">
-    <title> STRIKE Home Page</title>
-  </head><body link="#0000ee" text="#000000" vlink="#551a8b"
-alink="#ff0000" bgcolor="white">
-    <font face="Arial">
-    </font><center>
-<font face="Arial">
- <table width="80%" bgcolor="#ffebcd" border="1" bordercolor="#8b4513"
-cellpadding="15" cellspacing="0">
-	  <tbody><tr>
-	    <td>
-
-	      <table cellborder="0" valign="TOP" width="100%" border="0"
-cellpadding="15" cellspacing="0">
-		  <tbody><tr bgcolor="#ffebcd">
-		    <td colspan="1" width="5%" bgcolor="#ffebcd"><br></td>
-		    <td colspan="1" width="40%" bgcolor="#ffebcd"><br></td>
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-
-		    <td colspan="5" bgcolor="#ffebcd">
-		      <center><table><tbody><tr><td align="center"><b> <font
-color="#8b4513" size="7">STRIKE <br>A sequence alignment scoring tool</font></b></td></tr></tbody></table></center>
-		    </td>
-		  </tr>
-
-		  <tr>
-
-		    <td colspan="5" bgcolor="#ffebcd"><br></td>
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-		      <hr>
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-			<table cellborder="0" valign="top" width="100%" cellpadding="15"
-cellspacing="0">
-
-			    <tbody><tr align="center">
-
-			      <td onmouseover="style.backgroundColor='white';"
-onmouseout="style.backgroundColor='#FFE4C4'" width="15%"><b><a
-href="http://www.tcoffee.org/homepage.html"><font color="#8b4513">HOME</font></a></b></td>
-
-			      <td onmouseover="style.backgroundColor='white';"
-onmouseout="style.backgroundColor='#FFE4C4'" width="15%"><b><a
-href="#SERVERS"><font color="#8b4513">SERVERS</font></a></b></td>
-
-			      <td style="background-color: rgb(255, 228, 196);"
-onmouseover="style.backgroundColor='white';"
-onmouseout="style.backgroundColor='#FFE4C4'" width="15%"><b><a
-href="#DOWNLOAD"><font color="#8b4513">DOWNLOAD</font></a></b></td>
-			      <td style="background-color: rgb(255, 228, 196);"
-onmouseover="style.backgroundColor='white';"
-onmouseout="style.backgroundColor='#FFE4C4'" width="15%"><b><a
-href="#COMMANDS"><font color="#8b4513">DOCUMENTATION</font></a></b></td>
-
-
-			      <td onmouseover="style.backgroundColor='white';"
-onmouseout="style.backgroundColor='#FFE4C4'" width="15%"><b><a
-href="#CONTACT"><font color="#8b4513">CONTACT</font></a></b></td>
-
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-
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-		      </center>
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-		    <td rowspan="1" valign="top" bgcolor="white">
-
-		      <center><h2><font color="#8b4513">What is STRIKE?</font></h2></center>
-		      <table bgcolor="white">
-			  <tbody><tr>
-
-			    <td>
-			      <p align="justify">
-STRIKE (Single sTRucture Induced Evaluation) is a program to evaluate protein multiple sequence alignments using a single protein structure.
-</p>
-			      <!-- MAYBE .. ;) <p>A list of related publications is available <a href="http:">here</a> -->
-			    </td>
-
-			  </tr>
-		      </tbody></table>
-
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-
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-		    <td colspan="1" rowspan="1" bgcolor="white">
-
-		      <center><h2><font color="#8b4513"><a name="DOWNLOAD">DOWNLOAD</a></font></h2></center>
-		      <table bgcolor="white">
-			  <tbody><tr><td>
-
-			      <ul>
-				<li><b>Download the package <a target="_blank" href="./strike_v1.2.tar.bz2" target="_blank">here</a></b>
-			    </td></tr>
-
-		      </tbody></table>
-
-		    </td><td rowspan="3" bgcolor="#ffebcd"><br></td>
-		  </tr>
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-		      <center><h2><font color="#8b4513"><a name="INSTALLATION">INSTALLATION</a></font></h2></center>
-
-		      <table bgcolor="white">
-			  <tbody><tr>
-			    <td>
-			      <p align="justify">
-
-
-Typing 'make' in the command line will produce the executable.
-			      </p>
-
-			    </td>
-			  </tr>
-			  <tr>
-			    </tr><tr><td><br></td></tr>
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-		      <center><h2><font color="#8b4513">The Program</font></h2></center>
-
-		      <center><table bgcolor="white">
-			    <tbody><tr>
-			      <td>
-				<p align="justify">
-		STRIKE uses the STRIKE matrix to evaluate an alignment. This matrix gives a score for a contact similar to the Blosum matrix which gives a score to each nucleotide match. Contacts from the given structure are projected onto the alignment and each projected contact is scored.
-
-		The result is a single score for the whole alignment. The higher the score, the better is the agreement between alignmetn and structure.
-</p>
-			      </td>
-
-			    </tr>
-			</tbody></table></center>
-		    </td>
-
-		    <td colspan="1" rowspan="5" bgcolor="#ffebcd"><br></td>
-
-		    <td colspan="1" valign="top" bgcolor="white">
-
-		      <center><h2><font color="#8b4513"><a name="COMMANDS">DOCUMENTATION</a></font></h2></center>
-		      <table bgcolor="white">
-			  <tbody><tr>
-
-			    <td>
-			      <p> A detailed description is given in the incorporated Readme. The basic command is the following one:</p>
-
-			      <table width="100%" bgcolor="white" border="0" cellpadding="5">
-
-				  <tbody>
-
-<table bgcolor="white" border="0" cellpadding="5" width="100%">
-				  <tbody><tr>
-				    <td bgcolor="grey"></td>
-				  </tr>
-
-				  <tr>
-				    <td>Compute the score of an alignment:</td>
-
-				  </tr>
-
-				  <tr>
-				    <td>
-				       <code>  strike -c &lt;<i>template_file</i>&gt; -a  &lt;<i>alignment_file</i>&gt; </code>
-
-				    </td>
-
-				  </tr>
-				  <tr>
-
-				    <td bgcolor="grey"></td>
-</tr>
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-
-
-
-
-			      </tbody></table>
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-
-			    </td>
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-			  </tr>
-		      </tbody></table>
-		    </td>
-		    <td colspan="1" rowspan="5" bgcolor="#ffebcd"><br></td>
-		  </tr>
-
-		  <tr>
-		    <td colspan="1" bgcolor="#ffebcd"><br></td>
-
-		  </tr>
-
-		  <tr>
-
-		    <td valign="top" bgcolor="white">
-<!-- 		      <center><h2><font color="#8b4513"><a name="LINKS"  >LINKS</a></font></h2></center> -->
-		      <table bgcolor="white">
-
-			  <tbody><tr>
-
-			    <td>
-
-<!-- 			      <li><a href="http://rfam.sanger.ac.uk/" target="_blank">Rfam</a></li> -->
-<!-- <li><a href="http://infernal.janelia.org/" target="_blank">Infernal</a></li> -->
-<!-- <li><a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi" target="_blank">NCBI-Blast</a></li> -->
-
-<!-- <li><a href="http://www.advbiocomp.com/blast.html" target="_blank">AB-Blast</a></li> -->
-
-			    </td>
-
-			  </tr>
-		      </tbody></table>
-
-		    </td>
-		  </tr>
-
-		  <tr>
-		    <td colspan="1" bgcolor="#ffebcd"><br></td>
-		  </tr>
-
-		  <tr>
-
-		    <td valign="top" bgcolor="white">
-		      <center><h2><font color="#8b4513"><a name="CONTACT">CONTACT</a></font></h2></center>
-
-		      <table bgcolor="white">
-			  <tbody><tr>
-			    <td>
-			      <p>Our projects rely on your feeback. Please send me an
-				E-mail if you wish to make a request, a comment, or report a bug!
-				<code>
-				  <br><br>
-
-				  *******************************************<br>
-				  Dr. Cedric Notredame, PhD.                 <br>
-				  Group Leader                               <br>
-
-				  Comparative Bioinformatics Group           <br>
-				  Bioinformatics and Genomics Programme      <br>
-				  Center for Genomic Regulation (CRG)        <br>
-
-				  Dr Aiguader, 88                            <br>
-				  08003 Barcelona                            <br>
-
-				  Spain                                      <br>
-
-				  Email:  <a href="mailto:cedric.notredame@europe.com">cedric.notredame@europe.com</a>
-    <br>
-
-				  HOME :  <a href="http://www.tcoffee.org/homepage.html">http://www.tcoffee.org/homepage.html</a><br>
-
-				  GROUP:  <a
-href="http://pasteur.crg.es/portal/page/portal/Internet/02_Research/01_Programmes/01_Bioinformatics_Genomics/03_Comparative_Bioinformatics">CRG</a><br>
-
-				  Phone:  +34 933 160 271                <br>
-
-				  *******************************************       <br>
-
-				</code>
-			    </p></td>
-			  </tr>
-		      </tbody></table>
-
-		    </td>
-
-		  </tr>
-
-		  <tr>
-
-		    <td colspan="5" bgcolor="#ffebcd"><br></td>
-		  </tr>
-
-		  <tr>
-		    <td colspan="5" bgcolor="#ffe4c4">
-		      <center>
-			<hr>
-
-				<table cellborder="0" valign="top" width="100%" cellpadding="15"
-cellspacing="0">
-			    <tbody><tr align="center">
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-			      <td style="background-color: rgb(255, 228, 196);"
-onmouseover="style.backgroundColor='white';"
-onmouseout="style.backgroundColor='#FFE4C4'" width="15%"><b><a
-href="http://www.tcoffee.org/homepage.html"><font color="#8b4513">HOME</font></a></b></td>
-			      <td style="background-color: rgb(255, 228, 196);"
-onmouseover="style.backgroundColor='white';"
-onmouseout="style.backgroundColor='#FFE4C4'" width="15%"><b><a
-href="#SERVERS"><font color="#8b4513">SERVERS</font></a></b></td>
-			      <td style="background-color: rgb(255, 228, 196);"
-onmouseover="style.backgroundColor='white';"
-onmouseout="style.backgroundColor='#FFE4C4'" width="15%"><b><a
-href="#DOWNLOAD"><font color="#8b4513">DOWNLOAD</font></a></b></td>
-			      <td style="background-color: rgb(255, 228, 196);"
-onmouseover="style.backgroundColor='white';"
-onmouseout="style.backgroundColor='#FFE4C4'" width="15%"><b><a
-href="#COMMANDS"><font color="#8b4513">DOCUMENTATION</font></a></b></td>
-
-
-			      <td onmouseover="style.backgroundColor='white';"
-onmouseout="style.backgroundColor='#FFE4C4'" width="15%"><b><a
-href="#CONTACT"><font color="#8b4513">CONTACT</font></a></b></td>
-
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-
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-			<hr>
-		      </center>
-		    </td>
-  </tr>
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-<font face="Arial">  </font>
-  </body></html>
diff --git a/public_html/Projects/tcs/index (palestine.crg.es's conflicted copy 2016-05-05).html b/public_html/Projects/tcs/index (palestine.crg.es's conflicted copy 2016-05-05).html
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-<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<!-- saved from url=(0036)http://www.tcoffee.org/Projects/tcs/ -->
-<html><head><meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
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-<!--
-.tab { margin-left: 40px; }
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-    <title>Transitive Consistency Score Home Page</title>
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-	      <table width="100%" cellpadding="15" cellspacing="0" cellborder="0" valign="TOP" border="0">
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-		      <center><table><tbody><tr><td align="center"><b> <font size="7" color="#8B4513">TCS <br>Transitive Consistency Score for MSA evaluation</font></b></td></tr></tbody></table></center>
-		    </td>
-		  </tr>
-		  
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-		    <td colspan="5" bgcolor="#FFEBCD"><br></td>
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-			      <td width="15%" onmouseover="style.backgroundColor=&#39;white&#39;;" onmouseout="style.backgroundColor=&#39;#FFE4C4&#39;" style="background-color: rgb(255, 228, 196);"><b><a href="http://www.tcoffee.org/Projects/tcs/#SERVERS"><font color="#8B4513">SERVERS</font></a></b></td>
-			      <td width="15%" onmouseover="style.backgroundColor=&#39;white&#39;;" onmouseout="style.backgroundColor=&#39;#FFE4C4&#39;"><b><a href="http://www.tcoffee.org/Projects/tcs/#DOWNLOAD"><font color="#8B4513">DOWNLOAD</font></a></b></td>
-			      <td width="15%" onmouseover="style.backgroundColor=&#39;white&#39;;" onmouseout="style.backgroundColor=&#39;#FFE4C4&#39;"><b><a href="http://www.tcoffee.org/Projects/tcs/#COMMANDS"><font color="#8B4513">DOCUMENTATION</font></a></b></td>
-			      <td width="15%" onmouseover="style.backgroundColor=&#39;white&#39;;" onmouseout="style.backgroundColor=&#39;#FFE4C4&#39;"><b><a href="http://www.tcoffee.org/Projects/tcs/#OUTPUT"><font color="#8B4513">OUTPUT</font></a></b></td>
-			      <td width="15%" onmouseover="style.backgroundColor=&#39;white&#39;;" onmouseout="style.backgroundColor=&#39;#FFE4C4&#39;"><b><a href="http://www.tcoffee.org/Projects/tcs/#CONTACT"><font color="#8B4513">CONTACT</font></a></b></td>
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-		      <center><h2><font color="#8B4513">What is TCS?</font></h2></center>
-		      <table bgcolor="white">
-			  <tbody><tr>
-			      <td>
-				<p align="justify">TCS is an alignment evaluation score that makes it possible to identify in an MSA the most correct positions. It has been shown that these positions are the most likely to be structuraly correct and also the most informative when estimating phylogenetic trees. The TCS evaluation and filtering procedure is implemented in the T-Coffee package and can be used to evaluate and filter any third party multiple sequence alignment (including T-Coffee of course!).</p>
-				<p>A pre-print is available <a target="_blank" href="http://www.tcoffee.org/Publications/Pdf/062-MBE-TCS.preprint.pdf">here</a> and the final publication can be accessed from <a href="http://www.ncbi.nlm.nih.gov/pubmed/24694831">pubmed</a>.</p>
-				<p>A powerpoint is available <a target="_blank" href="201403_TCS_MBE.pptx">here</a>.</p>
-				<p><b>Please Cite:</b>TCS, A new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction. Chang JM, Tommaso PD, Notredame C., MBE (2014), doi: 10.1093/molbev/msu117<a href="http://www.ncbi.nlm.nih.gov/pubmed/24694831">pubmed</a></p>
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-		      <td colspan="1" rowspan="1" bgcolor="white">
-			<center><h2><font color="#8B4513"><a name="SERVERS">SERVERS</a></font></h2></center>
-			<table bgcolor="white">
-			  
-			  <tbody><tr><td>
-				<ul>
-				  <li><a href="http://tcoffee.crg.cat/tcs">http://tcoffee.crg.cat/tcs</a></li>
-				</ul>
-			      </td></tr>
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-		      </td><td rowspan="3" bgcolor="#FFEBCD"><br></td>
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-		      <center><h2><font color="#8B4513"><a name="DOWNLOAD">DOWNLOAD</a></font></h2></center>
-		      <table bgcolor="white">
-			  <tbody><tr><td>
-			      <ul>
-				<li>The tcs evaluation is a special mode of T-Coffee. To use it, download T-Coffee <a href="http://www.tcoffee.org/Packages/Beta/Latest/#DOWNLOAD">latest Beta Version</a> or check it out from <a href="https://github.com/cbcrg/tcoffee">Github</a>.</li>
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-			<center><h2><font color="#8B4513"><a name="INSTALLATION">INSTALLATION</a></font></h2></center>
-			<table bgcolor="white">
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-			      <td>
-				<p align="justify">Follow the standard T-Coffee <a href="http://www.tcoffee.org/Projects/tcoffee/index.html#INSTALLATION">installation procedure</a>.</p>
-			      </td>
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-			<center><h2><font color="#8B4513"><a name="INSTALLATION">USAGE</a></font></h2></center>
-			<table bgcolor="white" cellpadding="5">
-			  <tbody>
-			    <tr><td><p>All files used in the following examples can be downloaded from <a href="./files.tar.gz">here</a></p></td></tr>
-			    <tr><td bgcolor="grey"></td></tr>
-			    <tr><td><center><p><b>Evaluate an existing MSA</b></p></center></td></tr>
-			   
-			    <tr><td bgcolor="#d3d3d3"><p align="justify"><code>t_coffee -infile <i>prot.aln</i> -evaluate -output score_ascii, aln, score_html</code></p></td></tr>
-			    <tr><td><p><i>prot.score_ascii</i>: displays the score of the MSA, the sequences and theresiues. <b>This fille can be used to further filter your MSA with seq_reformat</b></p></td></tr>
-			    <tr><td><p><i>prot.score_html</i>: displays a colored version score of the MSA, the sequences and the resiues.</p></td></tr>
-			    <tr><td bgcolor="grey"></td></tr>
-			    
-			    <tr><td><center><p><b>Filter unreliable MSA positions</b></p></center></td></tr>
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -infile <i>prot.aln</i> -evaluate -output tcs_residue_filter3, tcs_column_filter3, tcs_residue_lower4</code></td></tr>
-			    <tr><td><p><i>prot.tcs_residue_filter3</i>: All residues with a TCS score lower than 3 are filtered out</b><p></td></tr>
-			    <tr><td><p><i>prot.tcs_column_filter3</i>: All columns with a TCS score lower than 3 are filtered out</b><p></td></tr>
-			    <tr><td><p><i>prot.tcs_residue_lower4</i>: All residues with a TCS score lower than 3 are lower cased</b><p></td></tr>
-			    <tr><td><p>Note that all these output functions are also compatible with the default T-Coffee when computing an alignment:<p></td></tr>
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -seq <i>prot.fa</i> -output tcs_residue_filter3, tcs_column_filter3, tcs_residue_lower4</code></td></tr>
-			    <tr><td><p>Or with seq_reformat using a T-Coffee <i>.score_ascii</i> file<p></td></tr>
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -other_pg seq_reformat -in <i>prot.aln</i> -struc_in <i>prot.score_ascii</i> -struc_in_f number_aln -output tcs_residue_filter3</code></td></tr>
-			    <tr><td bgcolor="grey"></td></tr>
-			    
-			    <tr><td><center><p><b>Weight MSA positions for Improved Trees</b><p></center></td></tr>
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -infile <i>prot.aln</i> -evaluate -output tcs_weighted, tcs_replicate_100</code></td></tr>
-			    <tr><td><p><i>prot.tcs_weighted</i>: All columns are duplicated according to their TCS score</b><p></td></tr>
-			    <tr><td><p><i>prot.tcs_replicate_100</i>:Contains 100 replicates in phylip format with each column drawn with a probability corresponding to its TCS score</b><p></td></tr>
-			    <tr><td><p><i>Note that all these output functions are also compatible with the default T-Coffee when computing an alignment:<p></td></tr>
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -seq <i>prot.fa</i> -output tcs_weighted, tcs_replicate_100</code></td></tr>
-			    <tr><td><p>Or with seq_reformat using a T-Coffee <i>.score_ascii</i> file<p></td></tr>
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -other_pg seq_reformat -in <i>prot.aln</i> -struc_in <i>prot.score_ascii</i> -struc_in_f number_aln -output tcs_weighted</code></td></tr>
-			    <tr><td bgcolor="grey"></td></tr>
-
-			    <tr><td><center><p><b>Work with coding DNA</b><p></center></td></tr>
-			    <tr><td><p>When working with DNA, it is advisable to first align the sequences at the protein level and later thread back the DNA onto your aligned proteins. The filtering must be done in two steps, as shown below. Note that your DNA and protein sequences must have the <b>same name</b></p></td></tr>
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -infile <i>prot.aln</i> -evaluate -output score_ascii</code></td></tr>
-			    <tr><td><p>This first step produces the TCS evaluation file <i>prot.score_ascii</i></p></td></tr>
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -other_pg seq_reformat -in <i>prot.aln</i> -in2 <i>dna.fa</i> -struc_in prot.score_ascii -struc_in_f number_aln -output tcs_replicate_100 -out <i>dna.replicates</i></code></td></tr>
-			    <tr><td><p><i>dna.replicates</i>: 100 DNA replicates with positions selected according to their AA TCS score</b><p></td></tr>
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -other_pg seq_reformat -in <i>prot.aln</i> -in2 <i>dna.fa</i> -struc_in prot.score_ascii -struc_in_f number_aln -output tcs_column_filter5 -out <i>dna.filter</i></code></td></tr>
-			    
-			    <tr><td><p><i>dna.filtered</i>: DNA positions filtered according to their TCS column score</b><p></td></tr>
-			    <tr><td bgcolor="grey"></td></tr>
-
-			    <tr><td><center><p><b>Using Different TCS Libraries</b></p></center></td></tr>
-			    <tr><td>It is possible to change the way TCS reliability is estimated. This can be done by building different T-Coffee libraries. The following instructions will do this.</td></tr>
-		      
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -infile <i>prot.aln</i> -evaluate <b>-method proba_pair</b> -output score_ascii, aln, score_html</code></td></tr>
-<tr><td><i>proba_pair</i> is the default mode of T-Coffee that runs a pair-HMM to populate the library with residue pairs having the best posterior probabilities.</td></tr>
-			    
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -infile <i>prot.aln</i> -evaluate <b>-method mafft_msa,kalign_msa,muscle_msa</b> -output score_ascii, aln, score_html</code></td></tr>
-<tr><td>This mode runs a series of fast multiple aligners. It is very fast and used by  <a href="http://www.ensembl.org/info/genome/compara/index.html">ENSEMBL Compara</a></td></tr>
-			    
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -infile <i>prot.aln</i> -evaluate <b>-method clustalw_pair,lalign_id_pair</b> -output score_ascii, aln, score_html</code></td></tr>
-			    <tr><td>This mode runs the orginal default T-Coffee that was combining local and global alignments.</a></td></tr>
-			    <tr><td bgcolor="grey"></td></tr>
-			    <tr><td><center><p><b>Summary of the Various Output Flags</b></p></center></td></tr>
-			    <tr><td>
-				<table border="1">
-				  <tbody>
-				    <tr><td><code>-output=score_ascii</code></td><td> outputs a TCS evaluation file</td></tr>
-				    <tr><td><code>-output=tcs_residue_filterN</code></td><td> Removes all <b>residues</b> with a TCS score lower than N</td></tr>
-				    <tr><td><code>-output=tcs_columns_filterN</code></td><td> Removes all <b>columns</b> with a TCS score lower than N</td></tr>
-				    <tr><td><code>-output=tcs_weighted</code></td><td> Duplicates all columns according to their TCS scoreN, The output is in Phylips</td></tr>
-				    <tr><td><code>-output=tcs_replicateN</code></td><td> Generates N phylips replicates, with columns drawn according to their TCS score</td></tr>
-				    <tr><td><code>-output=..._fasta</code></td><td>Generates the replicates or filtered output in FASTA</td></tr>
-				    <tr><td><code>-output=..._rphylip</code></td><td>Generates the -replicates or filtered output in a relaxed Phylip where names can be loguer than 10 char</td></tr>
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-		      <center><h2><font color="#8B4513"><a name="OUTPUT">OUTPUT</a></font></h2></center>
-		      <center><table bgcolor="white">
-			    <tbody>
-			      <tr>
-			      <td>
-				<p align="justify">Given an alignment file <a href='BB11001.aln' target='_blank'>BB11001.aln</a>, TCS outputs a file named <code>BB11001.score_html</code> that contains a color coded indicating the agreement between the library and the considered alignment. Red brick regions are in perfect transitive consistant relation between the library and the the input alignment, while blue regions have a very poor agreement.
-				Red brick regions can safely be assumed to be trusted while blue regions should be discarted. Green and Yellow regions should also be used with caution, especially when reconstructing a tree or building a profile. The top of the output provides the average conistency (0-100) for each sequence, thus indicating wether some sequences may have a less reliable alignment. A score lower than 50 should be considered poor.</p>
-				<img border="0" src="F4_scoreHtml.jpg">
-			      </td>
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-			      <td>
-				<p align="justify">Besides .score_html, there are other detailed outputs:				
-				  <ul>
-				    <li> <i>score_ascii</i> : contains ascii format for score_html.
-				    <li> <i>score_pdf</i> : will transfer score_html into pdf format.
-				    <li> <i>sp_ascii</i> : is a format reporting the TCS score of every aligned pair in the target MSA.
-				    <li> <i>tcs_column_filter2</i> : outputs an MSA in which columns having ColumnTCS lower than 2 are removed.
-				    <li> <i>tcs_weighted</i> : outputs an MSA in which columns are duplicated according to their ColumnTCS weight.
-				    <li> <i>tcs_replicate100</i> : outputs 100 replicate MSAs in which columns are randomly drawn according to their weights.
-				</ul>
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-		      <center><h2><font color="#8B4513"><a name="COMMANDS">DOCUMENTATION</a></font></h2></center>
-		      <table bgcolor="white">
-			  <tbody><tr>
-			    <td>
-			      <p>The full documentation is on the <a href="http://www.tcoffee.org/Projects/tcs/index.html#DOCUMENTATION">T-Coffee Homepage</a>. But the following shortcuts may be useful.</p>
-			      <table border="0" width="100%" cellpadding="5" bgcolor="white">
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-		      <center><h2><font color="#8B4513"><a name="LINKS">LINKS</a></font></h2></center>
-		      <table bgcolor="white">
-			  <tbody><tr>
-			    <td>
-			      structural validation
-			      <ul>
-			      <li><a href="http://lbgi.fr/balibase/">BAliBASE 3</a></li>
-			      <li><a href="http://www.drive5.com/bench/">PREFAB 4</a></li>
-			      </ul>
-			      phylogenetic validation
-			      <ul>
-				<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/18218900">yeasts</a> from Wong et al. Science, 2008</li>
-				<li><a href="geneList_YeastToL.txt">subset gene list </a> : at least one aligner yields a phylogeny topology identical to the canonical yeast ToL</li>
-			        <li><a href="http://molevol.cmima.csic.es/castresana/Gblocks.html">tips16</a> from Gblocks</li>
-			        <li><a href="http://trimal.cgenomics.org/">tips32, tips64</a> from trimAl</li>
-			      </ul>
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-		      <center><h2><font color="#8B4513"><a name="CONTACT">CONTACT</a></font></h2></center>
-		      <table bgcolor="white">
-			  <tbody><tr>
-			    <td>
-			      <p>Our projects relie on your feeback. Please send me an
-				E-mail if you wish to make a request, a comment, or report a bug! 
-				<code>
-				  <br><br>
-				  *******************************************<br>
-				  Dr. Cedric Notredame, PhD.                 <br>       
-				  Group Leader                               <br>
-				  Comparative Bioinformatics Group           <br>
-				  Bioinformatics and Genomics Programme      <br>
-				  Center for Genomic Regulation (CRG)        <br>
-				  Dr Aiguader, 88                            <br>
-				  08003 Barcelona                            <br>
-				  Spain                                      <br>
-				  Email:  <a href="mailto:cedric.notredame@europe.com">cedric.notredame@europe.com</a>    <br>
-				  HOME :  <a href="http://www.tcoffee.org/">http://www.tcoffee.org/</a><br>
-				  GROUP:  <a href="http://pasteur.crg.es/portal/page/portal/Internet/02_Research/01_Programmes/01_Bioinformatics_Genomics/03_Comparative_Bioinformatics">CRG</a><br>
-				  Phone:  +34 933 160 271                <br>
-				  *******************************************       <br>
-				</code>
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-			      <td width="15%" onmouseover="style.backgroundColor=&#39;white&#39;;" onmouseout="style.backgroundColor=&#39;#FFE4C4&#39;"><b><a href="http://www.tcoffee.org/Projects/homepage.html"><font color="#8B4513">HOME</font></a></b></td>
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-			      <td width="15%" onmouseover="style.backgroundColor=&#39;white&#39;;" onmouseout="style.backgroundColor=&#39;#FFE4C4&#39;"><b><a href="http://www.tcoffee.org/Projects/tcs/#DOWNLOAD"><font color="#8B4513">DOWNLOAD</font></a></b></td>
-			      <td width="15%" onmouseover="style.backgroundColor=&#39;white&#39;;" onmouseout="style.backgroundColor=&#39;#FFE4C4&#39;"><b><a href="http://www.tcoffee.org/Projects/tcs/#COMMANDS"><font color="#8B4513">DOCUMENTATION</font></a></b></td>
-			      <td width="15%" onmouseover="style.backgroundColor=&#39;white&#39;;" onmouseout="style.backgroundColor=&#39;#FFE4C4&#39;"><b><a href="http://www.tcoffee.org/Projects/tcs/#OUTPUT"><font color="#8B4513">OUTPUT</font></a></b></td>
-			      <td width="15%" onmouseover="style.backgroundColor=&#39;white&#39;;" onmouseout="style.backgroundColor=&#39;#FFE4C4&#39;"><b><a href="http://www.tcoffee.org/Projects/tcs/#CONTACT"><font color="#8B4513">CONTACT</font></a></b></td>
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-		      <center><table><tbody><tr><td align="center"><b> <font size="7" color="#8B4513">TCS <br>Transitive Consistency Score for MSA evaluation</font></b></td></tr></tbody></table></center>
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-		      <center><h2><font color="#8B4513">What is TCS?</font></h2></center>
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-				<p align="justify">TCS is an alignment evaluation score that makes it possible to identify in an MSA the most correct positions. It has been shown that these positions are the most likely to be structuraly correct and also the most informative when estimating phylogenetic trees. The TCS evaluation and filtering procedure is implemented in the T-Coffee package and can be used to evaluate and filter any third party multiple sequence alignment (including T-Coffee of course!).</p>
-				<p>A pre-print is available <a target="_blank" href="http://www.tcoffee.org/Publications/Pdf/062-MBE-TCS.preprint.pdf">here</a> and the final publication can be accessed from <a href="http://www.ncbi.nlm.nih.gov/pubmed/24694831">pubmed</a>.</p>
-				<p>A powerpoint is available <a target="_blank" href="201403_TCS_MBE.pptx">here</a>.</p>
-				<p><b>Please Cite:</b>TCS, A new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction. Chang JM, Tommaso PD, Notredame C., MBE (2014), doi: 10.1093/molbev/msu117<a href="http://www.ncbi.nlm.nih.gov/pubmed/24694831">pubmed</a></p>
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-				  <li><a href="http://tcoffee.crg.cat/tcs">http://tcoffee.crg.cat/tcs</a></li>
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-			      <ul>
-				<li>The tcs evaluation is a special mode of T-Coffee. To use it, download T-Coffee <a href="http://www.tcoffee.org/Packages/Beta/Latest/#DOWNLOAD">latest Beta Version</a> or check it out from <a href="https://github.com/cbcrg/tcoffee">Github</a>.</li>
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-			<center><h2><font color="#8B4513"><a name="INSTALLATION">INSTALLATION</a></font></h2></center>
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-				<p align="justify">Follow the standard T-Coffee <a href="http://www.tcoffee.org/Projects/tcoffee/index.html#INSTALLATION">installation procedure</a>.</p>
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-			<center><h2><font color="#8B4513"><a name="INSTALLATION">USAGE</a></font></h2></center>
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-			    <tr><td><p>All files used in the following examples can be downloaded from <a href="./files.tar.gz">here</a></p></td></tr>
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-			    <tr><td><center><p><b>Evaluate an existing MSA</b></p></center></td></tr>
-			   
-			    <tr><td bgcolor="#d3d3d3"><p align="justify"><code>t_coffee -infile <i>prot.aln</i> -evaluate -output score_ascii, aln, score_html</code></p></td></tr>
-			    <tr><td><p><i>prot.score_ascii</i>: displays the score of the MSA, the sequences and theresiues. <b>This fille can be used to further filter your MSA with seq_reformat</b></p></td></tr>
-			    <tr><td><p><i>prot.score_html</i>: displays a colored version score of the MSA, the sequences and the resiues.</p></td></tr>
-			    <tr><td bgcolor="grey"></td></tr>
-			    
-			    <tr><td><center><p><b>Filter unreliable MSA positions</b></p></center></td></tr>
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -infile <i>prot.aln</i> -evaluate -output tcs_residue_filter3, tcs_column_filter3, tcs_residue_lower4</code></td></tr>
-			    <tr><td><p><i>prot.tcs_residue_filter3</i>: All residues with a TCS score lower than 3 are filtered out</b><p></td></tr>
-			    <tr><td><p><i>prot.tcs_column_filter3</i>: All columns with a TCS score lower than 3 are filtered out</b><p></td></tr>
-			    <tr><td><p><i>prot.tcs_residue_lower4</i>: All residues with a TCS score lower than 3 are lower cased</b><p></td></tr>
-			    <tr><td><p>Note that all these output functions are also compatible with the default T-Coffee when computing an alignment:<p></td></tr>
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -seq <i>prot.fa</i> -output tcs_residue_filter3, tcs_column_filter3, tcs_residue_lower4</code></td></tr>
-			    <tr><td><p>Or with seq_reformat using a T-Coffee <i>.score_ascii</i> file<p></td></tr>
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -other_pg seq_reformat -in <i>prot.aln</i> -struc_in <i>prot.score_ascii</i> -struc_in_f number_aln -output tcs_residue_filter3</code></td></tr>
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-			    <tr><td><center><p><b>Weight MSA positions for Improved Trees</b><p></center></td></tr>
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -infile <i>prot.aln</i> -evaluate -output tcs_weighted, tcs_replicate_100</code></td></tr>
-			    <tr><td><p><i>prot.tcs_weighted</i>: All columns are duplicated according to their TCS score</b><p></td></tr>
-			    <tr><td><p><i>prot.tcs_replicate_100</i>:Contains 100 replicates in phylip format with each column drawn with a probability corresponding to its TCS score</b><p></td></tr>
-			    <tr><td><p><i>Note that all these output functions are also compatible with the default T-Coffee when computing an alignment:<p></td></tr>
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -seq <i>prot.fa</i> -output tcs_weighted, tcs_replicate_100</code></td></tr>
-			    <tr><td><p>Or with seq_reformat using a T-Coffee <i>.score_ascii</i> file<p></td></tr>
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -other_pg seq_reformat -in <i>prot.aln</i> -struc_in <i>prot.score_ascii</i> -struc_in_f number_aln -output tcs_weighted</code></td></tr>
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-			    <tr><td><center><p><b>Work with coding DNA</b><p></center></td></tr>
-			    <tr><td><p>When working with DNA, it is advisable to first align the sequences at the protein level and later thread back the DNA onto your aligned proteins. The filtering must be done in two steps, as shown below. Note that your DNA and protein sequences must have the <b>same name</b></p></td></tr>
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -infile <i>prot.aln</i> -evaluate -output score_ascii</code></td></tr>
-			    <tr><td><p>This first step produces the TCS evaluation file <i>prot.score_ascii</i></p></td></tr>
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -other_pg seq_reformat -in <i>prot.aln</i> -in2 <i>dna.fa</i> -struc_in prot.score_ascii -struc_in_f number_aln -output tcs_replicate_100 -out <i>dna.replicates</i></code></td></tr>
-			    <tr><td><p><i>dna.replicates</i>: 100 DNA replicates with positions selected according to their AA TCS score</b><p></td></tr>
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -other_pg seq_reformat -in <i>prot.aln</i> -in2 <i>dna.fa</i> -struc_in prot.score_ascii -struc_in_f number_aln -output tcs_column_filter5 -out <i>dna.filter</i></code></td></tr>
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-			    <tr><td><p><i>dna.filtered</i>: DNA positions filtered according to their TCS column score</b><p></td></tr>
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-
-			    <tr><td><center><p><b>Using Different TCS Libraries</b></p></center></td></tr>
-			    <tr><td>It is possible to change the way TCS reliability is estimated. This can be done by building different T-Coffee libraries. The following instructions will do this.</td></tr>
-		      
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -infile <i>prot.aln</i> -evaluate <b>-method proba_pair</b> -output score_ascii, aln, score_html</code></td></tr>
-<tr><td><i>proba_pair</i> is the default mode of T-Coffee that runs a pair-HMM to populate the library with residue pairs having the best posterior probabilities.</td></tr>
-			    
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -infile <i>prot.aln</i> -evaluate <b>-method mafft_msa,kalign_msa,muscle_msa</b> -output score_ascii, aln, score_html</code></td></tr>
-<tr><td>This mode runs a series of fast multiple aligners. It is very fast and used by  <a href="http://www.ensembl.org/info/genome/compara/index.html">ENSEMBL Compara</a></td></tr>
-			    
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -infile <i>prot.aln</i> -evaluate <b>-method clustalw_pair,lalign_id_pair</b> -output score_ascii, aln, score_html</code></td></tr>
-			    <tr><td>This mode runs the orginal default T-Coffee that was combining local and global alignments.</a></td></tr>
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-			    <tr><td><center><p><b>Summary of the Various Output Flags</b></p></center></td></tr>
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-				    <tr><td><code>-output=score_ascii</code></td><td> outputs a TCS evaluation file</td></tr>
-				    <tr><td><code>-output=tcs_residue_filterN</code></td><td> Removes all <b>residues</b> with a TCS score lower than N</td></tr>
-				    <tr><td><code>-output=tcs_columns_filterN</code></td><td> Removes all <b>columns</b> with a TCS score lower than N</td></tr>
-				    <tr><td><code>-output=tcs_weighted</code></td><td> Duplicates all columns according to their TCS scoreN, The output is in Phylips</td></tr>
-				    <tr><td><code>-output=tcs_replicateN</code></td><td> Generates N phylips replicates, with columns drawn according to their TCS score</td></tr>
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-		      <center><h2><font color="#8B4513"><a name="OUTPUT">OUTPUT</a></font></h2></center>
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-				<p align="justify">Given an alignment file <a href='BB11001.aln' target='_blank'>BB11001.aln</a>, TCS outputs a file named <code>BB11001.score_html</code> that contains a color coded indicating the agreement between the library and the considered alignment. Red brick regions are in perfect transitive consistant relation between the library and the the input alignment, while blue regions have a very poor agreement.
-				Red brick regions can safely be assumed to be trusted while blue regions should be discarted. Green and Yellow regions should also be used with caution, especially when reconstructing a tree or building a profile. The top of the output provides the average conistency (0-100) for each sequence, thus indicating wether some sequences may have a less reliable alignment. A score lower than 50 should be considered poor.</p>
-				<img border="0" src="F4_scoreHtml.jpg">
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-				<p align="justify">Besides .score_html, there are other detailed outputs:				
-				  <ul>
-				    <li> <i>score_ascii</i> : contains ascii format for score_html.
-				    <li> <i>score_pdf</i> : will transfer score_html into pdf format.
-				    <li> <i>sp_ascii</i> : is a format reporting the TCS score of every aligned pair in the target MSA.
-				    <li> <i>tcs_column_filter2</i> : outputs an MSA in which columns having ColumnTCS lower than 2 are removed.
-				    <li> <i>tcs_weighted</i> : outputs an MSA in which columns are duplicated according to their ColumnTCS weight.
-				    <li> <i>tcs_replicate100</i> : outputs 100 replicate MSAs in which columns are randomly drawn according to their weights.
-				</ul>
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-		      <center><h2><font color="#8B4513"><a name="COMMANDS">DOCUMENTATION</a></font></h2></center>
-		      <table bgcolor="white">
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-			    <td>
-			      <p>The full documentation is on the <a href="http://www.tcoffee.org/Projects/tcs/index.html#DOCUMENTATION">T-Coffee Homepage</a>. But the following shortcuts may be useful.</p>
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-		      <center><h2><font color="#8B4513"><a name="LINKS">LINKS</a></font></h2></center>
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-			    <td>
-			      structural validation
-			      <ul>
-			      <li><a href="http://lbgi.fr/balibase/">BAliBASE 3</a></li>
-			      <li><a href="http://www.drive5.com/bench/">PREFAB 4</a></li>
-			      </ul>
-			      phylogenetic validation
-			      <ul>
-				<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/18218900">yeasts</a> from Wong et al. Science, 2008</li>
-				<li><a href="geneList_YeastToL.txt">subset gene list </a> : at least one aligner yields a phylogeny topology identical to the canonical yeast ToL</li>
-			        <li><a href="http://molevol.cmima.csic.es/castresana/Gblocks.html">tips16</a> from Gblocks</li>
-			        <li><a href="http://trimal.cgenomics.org/">tips32, tips64</a> from trimAl</li>
-			      </ul>
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-		      <center><h2><font color="#8B4513"><a name="CONTACT">CONTACT</a></font></h2></center>
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-			    <td>
-			      <p>Our projects relie on your feeback. Please send me an
-				E-mail if you wish to make a request, a comment, or report a bug! 
-				<code>
-				  <br><br>
-				  *******************************************<br>
-				  Dr. Cedric Notredame, PhD.                 <br>       
-				  Group Leader                               <br>
-				  Comparative Bioinformatics Group           <br>
-				  Bioinformatics and Genomics Programme      <br>
-				  Center for Genomic Regulation (CRG)        <br>
-				  Dr Aiguader, 88                            <br>
-				  08003 Barcelona                            <br>
-				  Spain                                      <br>
-				  Email:  <a href="mailto:cedric.notredame@europe.com">cedric.notredame@europe.com</a>    <br>
-				  HOME :  <a href="http://www.tcoffee.org/">http://www.tcoffee.org/</a><br>
-				  GROUP:  <a href="http://pasteur.crg.es/portal/page/portal/Internet/02_Research/01_Programmes/01_Bioinformatics_Genomics/03_Comparative_Bioinformatics">CRG</a><br>
-				  Phone:  +34 933 160 271                <br>
-				  *******************************************       <br>
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-		      <center><table><tbody><tr><td align="center"><b> <font size="7" color="#8B4513">TCS <br>Transitive Consistency Score for MSA evaluation</font></b></td></tr></tbody></table></center>
-		    </td>
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-			      <td width="15%" onmouseover="style.backgroundColor=&#39;white&#39;;" onmouseout="style.backgroundColor=&#39;#FFE4C4&#39;"><b><a href="http://www.tcoffee.org/Projects/tcs/#CONTACT"><font color="#8B4513">CONTACT</font></a></b></td>
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-		      <center><h2><font color="#8B4513">What is TCS?</font></h2></center>
-		      <table bgcolor="white">
-			  <tbody><tr>
-			    <td>
-			      <p align="justify">TCS is an alignment evaluation score that mes it possible to identify the positions most likely to be structuraly correct as well most likely to yield an improved phylogenetic tree. The TCS evaluation and filtering procedure is implemented in the T-Coffee package and can be used to evaluate and filter any third party multiple sequence alignment (including T-Coffee of course!).</p>
-			      <p>A pre-print is available <a target="_blank" href="http://www.tcoffee.org/Publications/Pdf/062-MBE-TCS.preprint.pdf">here</a>.</p>
-			      <p>A powerpoint is available <a target="_blank" href="201403_TCS_MBE.pptx">here</a>.</p>
-			    </td>
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-		      <table bgcolor="white">
-			
-			  <tbody><tr><td>
-			      <ul>
-				<li><a href="http://tcoffee.crg.cat/tcs">http://tcoffee.crg.cat/tcs</a></li>
-			      </ul>
-			    </td></tr>
-		      </tbody></table>
-		    </td><td rowspan="3" bgcolor="#FFEBCD"><br></td>
-		  </tr>
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-		      <center><h2><font color="#8B4513"><a name="DOWNLOAD">DOWNLOAD</a></font></h2></center>
-		      <table bgcolor="white">
-			  <tbody><tr><td>
-			      <ul>
-				<li>The tcs evaluation is only a special mode of T-Coffee. Download the latest T-Coffee version <a href="http://www.tcoffee.org/Projects/tcoffee/index.html#DOWNLOAD">here</a>.</li>
-			      </ul>
-			    </td></tr>
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-		    <td colspan="3" bgcolor="white" valign="top">
-		      <center><h2><font color="#8B4513"><a name="INSTALLATION">INSTALLATION</a></font></h2></center>
-		      <table bgcolor="white">
-			  <tbody><tr>
-			    <td>
-			      <p align="justify">Follow the standard T-Coffee <a href="http://www.tcoffee.org/Projects/tcoffee/index.html#INSTALLATION">installation procedure</a>.</p>
-			    </td>
-			  </tr>
-		      </tbody></table>
-		    </td>
-		    <td bgcolor="#FFEBCD"><br></td>
-		  </tr>
-		    
-
-
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-		    <td colspan="1" rowspan="5" bgcolor="#FFEBCD"><br></td>
-		    <td colspan="1" rowspan="5" bgcolor="white" valign="top">
-		      <center><h2><font color="#8B4513"><a name="OUTPUT">OUTPUT</a></font></h2></center>
-		      <center><table bgcolor="white">
-			    <tbody>
-			      <tr>
-			      <td>
-				<p align="justify">Given an alignment file <a href='BB11001.aln' target='_blank'>BB11001.aln</a>, TCS outputs a file named <code>BB11001.score_html</code> that contains a color coded indicating the agreement between the library and the considered alignment. Red brick regions are in perfect transitive consistant relation between the library and the the input alignment, while blue regions have a very poor agreement.
-				Red brick regions can safely be assumed to be trusted while blue regions should be discarted. Green and Yellow regions should also be used with caution, especially when reconstructing a tree or building a profile. The top of the output provides the average conistency (0-100) for each sequence, thus indicating wether some sequences may have a less reliable alignment. A score lower than 50 should be considered poor.</p>
-				<img border="0" src="F4_scoreHtml.jpg">
-			      </td>
-			    </tr>
-			    <tr>
-			      <td>
-				<p align="justify">Besides .score_html, there are other detailed outputs:				
-				  <ul>
-				    <li> <i>score_ascii</i> : contains ascii format for score_html.
-				    <li> <i>score_pdf</i> : will transfer score_html into pdf format.
-				    <li> <i>sp_ascii</i> : is a format reporting the TCS score of every aligned pair in the target MSA.
-				    <li> <i>tcs_column_filter2</i> : outputs an MSA in which columns having ColumnTCS lower than 2 are removed.
-				    <li> <i>tcs_weighted</i> : outputs an MSA in which columns are duplicated according to their ColumnTCS weight.
-				    <li> <i>tcs_replicate100</i> : outputs 100 replicate MSAs in which columns are randomly drawn according to their weights.
-				</ul>
-			      </td>
-			    </tr>  
-			      
-			</tbody></table></center>
-		    </td>
-		    <td colspan="1" rowspan="5" bgcolor="#FFEBCD"><br></td>
-		    <td colspan="1" bgcolor="white" valign="top">
-		      <center><h2><font color="#8B4513"><a name="COMMANDS">DOCUMENTATION</a></font></h2></center>
-		      <table bgcolor="white">
-			  <tbody><tr>
-			    <td>
-			      <p>The full documentation is on the <a href="http://www.tcoffee.org/Projects/tcs/index.html#DOCUMENTATION">T-Coffee Homepage</a>. But the following shortcuts may be useful.</p>
-			      <table border="0" width="100%" cellpadding="5" bgcolor="white">
-				  <tbody><tr>
-				    <td bgcolor="grey"></td>
-				  </tr>
-				  <tr>
-				    <td>To run the current default T-Coffee whose libraries are populated using the ProbCons pair-HMM, type</td>
-				  </tr>
-				  <tr>
-				    <td>
-				      <code> t_coffee -infile <i>BB11001.aln</i> -evaluate -method proba_pair</code>
-				    </td>
-				  </tr>
-				  <tr>
-				    <td bgcolor="grey"></td>
-				  </tr>
-				  <tr>
-				    <td>This protocol corresponds to the original T-Coffee. It involves computing all pairwise alignments using ClustalW and Lalign, type</td>
-				  </tr>
-				  <tr>
-				    <td>
-				      <code> t_coffee -infile <i>BB11001.aln</i> -evaluate -method clustalw_pair,lalign_id_pair</code>
-				    </td>
-				  </tr>
-				  <tr>
-				    <td colspan="3" bgcolor="grey"></td>
-				  </tr>
-				  <tr>
-				    <td>This protocol uses the procedure developed for the Ensembl Compara pipeline and relies on generating MSAs using fast aligners: MAFFT, MUSCLE and Kalign, type</td>
-				  </tr>
-				  <tr>
-				    <td>
-				      <code> t_coffee -infile <i>BB11001.aln</i> -evaluate -method kafft_msa,kalign_msa,muscle_msa</code>
-				    </td>
-				  </tr>
-				  <tr>
-				    <td colspan="3" bgcolor="grey"></td>
-				  </tr>
-			      </tbody></table>
-			      
-			    </td>
-			  </tr>
-		      </tbody></table>
-		    </td>
-		    <td colspan="1" rowspan="5" bgcolor="#FFEBCD"><br></td>
-		  </tr>
-		  <tr>
-		    <td colspan="1" bgcolor="#FFEBCD"><br></td>
-		  </tr>
-		  
-		  <tr>
-		    <td bgcolor="white" valign="top">
-		      <center><h2><font color="#8B4513"><a name="LINKS">LINKS</a></font></h2></center>
-		      <table bgcolor="white">
-			  <tbody><tr>
-			    <td>
-			      structural validation
-			      <ul>
-			      <li><a href="http://lbgi.fr/balibase/">BAliBASE 3</a></li>
-			      <li><a href="http://www.drive5.com/bench/">PREFAB 4</a></li>
-			      </ul>
-			      phylogenetic validation
-			      <ul>
-				<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/18218900">yeasts</a> from Wong et al. Science, 2008</li>
-				<li><a href="geneList_YeastToL.txt">subset gene list </a> : at least one aligner yields a phylogeny topology identical to the canonical yeast ToL</li>
-			        <li><a href="http://molevol.cmima.csic.es/castresana/Gblocks.html">tips16</a> from Gblocks</li>
-			        <li><a href="http://trimal.cgenomics.org/">tips32, tips64</a> from trimAl</li>
-			      </ul>
-			    </td>
-			  </tr>
-		      </tbody></table>
-		    </td>
-		  </tr>
-		  
-		  <tr>
-		    <td colspan="1" bgcolor="#FFEBCD"><br></td>
-		  </tr>
-		  <tr>
-		    <td bgcolor="white" valign="top">
-		      <center><h2><font color="#8B4513"><a name="CONTACT">CONTACT</a></font></h2></center>
-		      <table bgcolor="white">
-			  <tbody><tr>
-			    <td>
-			      <p>Our projects relie on your feeback. Please send me an
-				E-mail if you wish to make a request, a comment, or report a bug! 
-				<code>
-				  <br><br>
-				  *******************************************<br>
-				  Dr. Cedric Notredame, PhD.                 <br>       
-				  Group Leader                               <br>
-				  Comparative Bioinformatics Group           <br>
-				  Bioinformatics and Genomics Programme      <br>
-				  Center for Genomic Regulation (CRG)        <br>
-				  Dr Aiguader, 88                            <br>
-				  08003 Barcelona                            <br>
-				  Spain                                      <br>
-				  Email:  <a href="mailto:cedric.notredame@europe.com">cedric.notredame@europe.com</a>    <br>
-				  HOME :  <a href="http://www.tcoffee.org/">http://www.tcoffee.org/</a><br>
-				  GROUP:  <a href="http://pasteur.crg.es/portal/page/portal/Internet/02_Research/01_Programmes/01_Bioinformatics_Genomics/03_Comparative_Bioinformatics">CRG</a><br>
-				  Phone:  +34 933 160 271                <br>
-				  *******************************************       <br>
-				</code>
-			    </p></td>
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-			      <td width="15%" onmouseover="style.backgroundColor=&#39;white&#39;;" onmouseout="style.backgroundColor=&#39;#FFE4C4&#39;"><b><a href="http://www.tcoffee.org/Projects/tcs/#OUTPUT"><font color="#8B4513">OUTPUT</font></a></b></td>
-			      <td width="15%" onmouseover="style.backgroundColor=&#39;white&#39;;" onmouseout="style.backgroundColor=&#39;#FFE4C4&#39;"><b><a href="http://www.tcoffee.org/Projects/tcs/#CONTACT"><font color="#8B4513">CONTACT</font></a></b></td>
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-		      <center><table><tbody><tr><td align="center"><b> <font size="7" color="#8B4513">TCS <br>Transitive Consistency Score for MSA evaluation</font></b></td></tr></tbody></table></center>
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-		      <center><h2><font color="#8B4513">What is TCS?</font></h2></center>
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-			      <p align="justify">TCS is an alignment evaluation score that mes it possible to identify the positions most likely to be structuraly correct as well most likely to yield an improved phylogenetic tree. The TCS evaluation and filtering procedure is implemented in the T-Coffee package and can be used to evaluate and filter any third party multiple sequence alignment (including T-Coffee of course!).</p>
-			      <p>A pre-print is available <a target="_blank" href="http://www.tcoffee.org/Publications/Pdf/062-MBE-TCS.preprint.pdf">here</a>.</p>
-			      <p>A powerpoint is available <a target="_blank" href="201403_TCS_MBE.pptx">here</a>.</p>
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-				<li><a href="http://tcoffee.crg.cat/tcs">http://tcoffee.crg.cat/tcs</a></li>
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-			      <ul>
-				<li>The tcs evaluation is only a special mode of T-Coffee. Download the latest T-Coffee version <a href="http://www.tcoffee.org/Projects/tcoffee/index.html#DOWNLOAD">here</a>.</li>
-			      </ul>
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-		      <center><h2><font color="#8B4513"><a name="INSTALLATION">INSTALLATION</a></font></h2></center>
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-			    <td>
-			      <p align="justify"><b>1-</b>Follow the standard T-Coffee <a href="http://www.tcoffee.org/Projects/tcoffee/index.html#INSTALLATION">installation procedure</a>.</p>
-			    </td>
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-		      <center><h2><font color="#8B4513"><a name="OUTPUT">OUTPUT</a></font></h2></center>
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-				<p align="justify">Given an alignment file <a href='BB11001.aln' target='_blank'>BB11001.aln</a>, TCS outputs a file named <code>BB11001.score_html</code> that contains a color coded indicating the agreement between the library and the considered alignment. Red brick regions are in perfect transitive consistant relation between the library and the the input alignment, while blue regions have a very poor agreement.
-				Red brick regions can safely be assumed to be trusted while blue regions should be discarted. Green and Yellow regions should also be used with caution, especially when reconstructing a tree or building a profile. The top of the output provides the average conistency (0-100) for each sequence, thus indicating wether some sequences may have a less reliable alignment. A score lower than 50 should be considered poor.</p>
-				<img border="0" src="F4_scoreHtml.jpg">
-			      </td>
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-				<p align="justify">Besides .score_html, there are other detailed outputs:				
-				  <ul>
-				    <li> <i>score_ascii</i> : contains ascii format for score_html.
-				    <li> <i>score_pdf</i> : will transfer score_html into pdf format.
-				    <li> <i>sp_ascii</i> : is a format reporting the TCS score of every aligned pair in the target MSA.
-				    <li> <i>tcs_column_filter2</i> : outputs an MSA in which columns having ColumnTCS lower than 2 are removed.
-				    <li> <i>tcs_weighted</i> : outputs an MSA in which columns are duplicated according to their ColumnTCS weight.
-				    <li> <i>tcs_replicate100</i> : outputs 100 replicate MSAs in which columns are randomly drawn according to their weights.
-				</ul>
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-		      <center><h2><font color="#8B4513"><a name="COMMANDS">DOCUMENTATION</a></font></h2></center>
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-			      <p>The full documentation is on the <a href="http://www.tcoffee.org/Projects/tcs/index.html#DOCUMENTATION">T-Coffee Homepage</a>. But the following shortcuts may be useful.</p>
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-				    <td>To run the current default T-Coffee whose libraries are populated using the ProbCons pair-HMM, type</td>
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-				    <td>
-				      <code> t_coffee -infile <i>BB11001.aln</i> -evaluate -method proba_pair</code>
-				    </td>
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-				    <td bgcolor="grey"></td>
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-				    <td>This protocol corresponds to the original T-Coffee. It involves computing all pairwise alignments using ClustalW and Lalign, type</td>
-				  </tr>
-				  <tr>
-				    <td>
-				      <code> t_coffee -infile <i>BB11001.aln</i> -evaluate -method clustalw_pair,lalign_id_pair</code>
-				    </td>
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-				  <tr>
-				    <td colspan="3" bgcolor="grey"></td>
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-				    <td>This protocol uses the procedure developed for the Ensembl Compara pipeline and relies on generating MSAs using fast aligners: MAFFT, MUSCLE and Kalign, type</td>
-				  </tr>
-				  <tr>
-				    <td>
-				      <code> t_coffee -infile <i>BB11001.aln</i> -evaluate -method kafft_msa,kalign_msa,muscle_msa</code>
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-		      <center><h2><font color="#8B4513"><a name="LINKS">LINKS</a></font></h2></center>
-		      <table bgcolor="white">
-			  <tbody><tr>
-			    <td>
-			      structural validation
-			      <ul>
-			      <li><a href="http://lbgi.fr/balibase/">BAliBASE 3</a></li>
-			      <li><a href="http://www.drive5.com/bench/">PREFAB 4</a></li>
-			      </ul>
-			      phylogenetic validation
-			      <ul>
-				<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/18218900">yeasts</a> from Wong et al. Science, 2008</li>
-				<li><a href="geneList_YeastToL.txt">subset gene list </a> : at least one aligner yields a phylogeny topology identical to the canonical yeast ToL</li>
-			        <li><a href="http://molevol.cmima.csic.es/castresana/Gblocks.html">tips16</a> from Gblocks</li>
-			        <li><a href="http://trimal.cgenomics.org/">tips32, tips64</a> from trimAl</li>
-			      </ul>
-			    </td>
-			  </tr>
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-			      <p>Our projects relie on your feeback. Please send me an
-				E-mail if you wish to make a request, a comment, or report a bug! 
-				<code>
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-				  *******************************************<br>
-				  Dr. Cedric Notredame, PhD.                 <br>       
-				  Group Leader                               <br>
-				  Comparative Bioinformatics Group           <br>
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-				  Dr Aiguader, 88                            <br>
-				  08003 Barcelona                            <br>
-				  Spain                                      <br>
-				  Email:  <a href="mailto:cedric.notredame@europe.com">cedric.notredame@europe.com</a>    <br>
-				  HOME :  <a href="http://www.tcoffee.org/">http://www.tcoffee.org/</a><br>
-				  GROUP:  <a href="http://pasteur.crg.es/portal/page/portal/Internet/02_Research/01_Programmes/01_Bioinformatics_Genomics/03_Comparative_Bioinformatics">CRG</a><br>
-				  Phone:  +34 933 160 271                <br>
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-		      <center><table><tbody><tr><td align="center"><b> <font size="7" color="#8B4513">TCS <br>Transitive Consistency Score for MSA evaluation</font></b></td></tr></tbody></table></center>
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-			      <td width="15%" onmouseover="style.backgroundColor=&#39;white&#39;;" onmouseout="style.backgroundColor=&#39;#FFE4C4&#39;"><b><a href="http://www.tcoffee.org/Projects/homepage.html"><font color="#8B4513">HOME</font></a></b></td>
-			      <td width="15%" onmouseover="style.backgroundColor=&#39;white&#39;;" onmouseout="style.backgroundColor=&#39;#FFE4C4&#39;" style="background-color: rgb(255, 228, 196);"><b><a href="http://www.tcoffee.org/Projects/tcs/#SERVERS"><font color="#8B4513">SERVERS</font></a></b></td>
-			      <td width="15%" onmouseover="style.backgroundColor=&#39;white&#39;;" onmouseout="style.backgroundColor=&#39;#FFE4C4&#39;"><b><a href="http://www.tcoffee.org/Projects/tcs/#DOWNLOAD"><font color="#8B4513">DOWNLOAD</font></a></b></td>
-			      <td width="15%" onmouseover="style.backgroundColor=&#39;white&#39;;" onmouseout="style.backgroundColor=&#39;#FFE4C4&#39;"><b><a href="http://www.tcoffee.org/Projects/tcs/#COMMANDS"><font color="#8B4513">DOCUMENTATION</font></a></b></td>
-			      <td width="15%" onmouseover="style.backgroundColor=&#39;white&#39;;" onmouseout="style.backgroundColor=&#39;#FFE4C4&#39;"><b><a href="http://www.tcoffee.org/Projects/tcs/#OUTPUT"><font color="#8B4513">OUTPUT</font></a></b></td>
-			      <td width="15%" onmouseover="style.backgroundColor=&#39;white&#39;;" onmouseout="style.backgroundColor=&#39;#FFE4C4&#39;"><b><a href="http://www.tcoffee.org/Projects/tcs/#CONTACT"><font color="#8B4513">CONTACT</font></a></b></td>
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-		      <center><h2><font color="#8B4513">What is TCS?</font></h2></center>
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-				<p align="justify">TCS is an alignment evaluation score that makes it possible to identify in an MSA the most correct positions. It has been shown that these positions are the most likely to be structuraly correct and also the most informative when estimating phylogenetic trees. The TCS evaluation and filtering procedure is implemented in the T-Coffee package and can be used to evaluate and filter any third party multiple sequence alignment (including T-Coffee of course!).</p>
-				<p>A pre-print is available <a target="_blank" href="http://www.tcoffee.org/Publications/Pdf/062-MBE-TCS.preprint.pdf">here</a> and the final publication can be accessed from <a href="http://www.ncbi.nlm.nih.gov/pubmed/24694831">pubmed</a>.</p>
-				<p>A powerpoint is available <a target="_blank" href="201403_TCS_MBE.pptx">here</a>.</p>
-				<p><b>Please Cite:</b>TCS, A new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction. Chang JM, Tommaso PD, Notredame C., MBE (2014), doi: 10.1093/molbev/msu117<a href="http://www.ncbi.nlm.nih.gov/pubmed/24694831">pubmed</a></p>
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-		      <td colspan="1" rowspan="1" bgcolor="white">
-			<center><h2><font color="#8B4513"><a name="SERVERS">SERVERS</a></font></h2></center>
-			<table bgcolor="white">
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-			  <tbody><tr><td>
-				<ul>
-				  <li><a href="http://tcoffee.crg.cat/tcs">http://tcoffee.crg.cat/tcs</a></li>
-				</ul>
-			      </td></tr>
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-		      <center><h2><font color="#8B4513"><a name="DOWNLOAD">DOWNLOAD</a></font></h2></center>
-		      <table bgcolor="white">
-			  <tbody><tr><td>
-			      <ul>
-				<li>The tcs evaluation is a special mode of T-Coffee. To use it, download the latest T-Coffee version <a href="http://www.tcoffee.org/Projects/tcoffee/index.html#DOWNLOAD">here</a>.</li>
-			      </ul>
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-			<center><h2><font color="#8B4513"><a name="INSTALLATION">INSTALLATION</a></font></h2></center>
-			<table bgcolor="white">
-			  <tbody><tr>
-			      <td>
-				<p align="justify">Follow the standard T-Coffee <a href="http://www.tcoffee.org/Projects/tcoffee/index.html#INSTALLATION">installation procedure</a>.</p>
-			      </td>
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-			<center><h2><font color="#8B4513"><a name="INSTALLATION">USAGE</a></font></h2></center>
-			<table bgcolor="white" cellpadding="5">
-			  <tbody>
-			    <tr><td><p>All files used in the following examples can be downloaded from <a href="./files.tar.gz">here</a></p></td></tr>
-			    <tr><td bgcolor="grey"></td></tr>
-			    <tr><td><center><p><b>Evaluate an existing MSA</b></p></center></td></tr>
-			   
-			    <tr><td bgcolor="#d3d3d3"><p align="justify"><code>t_coffee -infile <i>test.prot.aln</i> -evaluate -output score_ascii, aln, score_html</code></p></td></tr>
-			    <tr><td><p><i>test.prot.score_ascii</i>: displays the score of the MSA, the sequences and theresiues. <b>This fille can be used to further filter your MSA with seq_reformat</b></p></td></tr>
-			    <tr><td><p><i>test.prot.score_html</i>: displays a colored version score of the MSA, the sequences and the resiues.</p></td></tr>
-			    <tr><td bgcolor="grey"></td></tr>
-			    
-			    <tr><td><center><p><b>Filter unreliable MSA positions</b></p></center></td></tr>
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -infile <i>test.prot.aln</i> -evaluate -output tcs_residue_filter3, tcs_column_filter3, tcs_residue_lower4</code></td></tr>
-			    <tr><td><p><i>test.prot.tcs_residue_filter3</i>: All residues with a TCS score lower than 3 are filtered out</b><p></td></tr>
-			    <tr><td><p><i>test.prot.tcs_column_filter3</i>: All columns with a TCS score lower than 3 are filtered out</b><p></td></tr>
-			    <tr><td><p><i>test.prot.tcs_residue_lower4</i>: All residues with a TCS score lower than 3 are lower cased</b><p></td></tr>
-			    <tr><td><p>Note that all these outpout functions are also compatible with the default T-Coffee when computing an alignment:<p></td></tr>
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -seq <i>test.prot.fa</i> -output tcs_residue_filter3, tcs_column_filter3, tcs_residue_lower4</code></td></tr>
-			    <tr><td><p>Or with seq_reformat using a T-Coffee <i>.score_ascii</i> file<p></td></tr>
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -other_pg seq_reformat -in <i>test.prot.aln</i> -struc_in <i>test.prot.score_ascii</i> -struc_in_f number_aln -output tcs_residue_filter3</code></td></tr>
-			    <tr><td bgcolor="grey"></td></tr>
-			    
-			    <tr><td><center><p><b>Weight MSA positions for Improved Trees</b><p></center></td></tr>
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -infile <i>test.prot.aln</i> -evaluate -output tcs_weighted, tcs_replicate_100</code></td></tr>
-			    <tr><td><p><i>test.prot.tcs_weighted</i>: All columns are duplicated according to their TCS score</b><p></td></tr>
-			    <tr><td><p><i>test.prot.tcs_replicate_100</i>:Contains 100 replicates in phylip format with each column drawn with a probability corresponding to its TCS score</b><p></td></tr>
-			    <tr><td><p><i>Note that all these outpout functions are also compatible with the default T-Coffee when computing an alignment:<p></td></tr>
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -seq <i>test.prot.fa</i> -output tcs_weighted, tcs_replicate_100</code></td></tr>
-			    <tr><td><p>Or with seq_reformat using a T-Coffee <i>.score_ascii</i> file<p></td></tr>
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -other_pg seq_reformat -in <i>test.prot.aln</i> -struc_in <i>test.prot.score_ascii</i> -struc_in_f number_aln -output tcs_weighted</code></td></tr>
-			    <tr><td bgcolor="grey"></td></tr>
-
-			    <tr><td><center><p><b>Work with coding DNA</b><p></center></td></tr>
-			    <tr><td><p>When working with DNA, it is advisable to first align the sequences at the protein level and later thread back the DNA onto your aligned proteins. The filtering must be done in two steps, as shown below. Note that your DNA and protein sequences must have the <b>same name</b></p></td></tr>
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -infile <i>test.prot.aln</i> -evaluate -output score_ascii</code></td></tr>
-			    <tr><td><p>This first step produces the TCS evaluation file <i>test.prot.score_ascii</i></p></td></tr>
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -other_pg seq_reformat -in <i>test.prot.aln</i> -in2 <i>test.dna.fa</i> -struc_in test.prot.score_ascii -struc_in_f number_aln -output tcs_replicate_100 -out <i>test.dna.replicates</i></code></td></tr>
-			    <tr><td><p><i>test.dna.replicates</i>: 100 DNA replicates with positions selected according to their AA TCS score</b><p></td></tr>
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -other_pg seq_reformat -in <i>test.prot.aln</i> -in2 <i>test.dna.fa</i> -struc_in test.prot.score_ascii -struc_in_f number_aln -output tcs_column_filter5 -out <i>test.dna.filter</i></code></td></tr>
-			    
-			    <tr><td><p><i>test.dna.filtered</i>: DNA positions filtered according to their TCS column score</b><p></td></tr>
-			    <tr><td bgcolor="grey"></td></tr>
-
-			    <tr><td><center><p><b>Using Different TCS Libraries</b></p></center></td></tr>
-			    <tr><td>It is possible to change the way TCS reliability is estimated. This can be done by building different T-Coffee libraries. The following instructions will do this.</td></tr>
-		      
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -infile <i>test.aln</i> -evaluate <b>-method proba_pair</b> -output score_ascii, aln, score_html</code></td></tr>
-<tr><td><i>proba_pair</i> is the default mode of T-Coffee that runs a pair-HMM to populate the library with residue pairs having the best posterior probabilities.</td></tr>
-			    
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -infile <i>test.aln</i> -evaluate <b>-method mafft_msa,kalign_msa,muscle_msa</b> -output score_ascii, aln, score_html</code></td></tr>
-<tr><td>This mode runs a series of fast multiple aligners. It is very fast and used by  <a href="http://www.ensembl.org/info/genome/compara/index.html">ENSEMBL Compara</a></td></tr>
-			    
-			    <tr><td bgcolor="#d3d3d3"><code>t_coffee -infile <i>test.aln</i> -evaluate <b>-method clustalw_pair,lalign_id_pair</b> -output score_ascii, aln, score_html</code></td></tr>
-			    <tr><td>This mode runs the orginal default T-Coffee that was combining local and global alignments.</a></td></tr>
-			    <tr><td bgcolor="grey"></td></tr>
-			    <tr><td><center><p><b>Summary of the Various Output Flags</b></p></center></td></tr>
-			    <tr><td>
-				<table border="1">
-				  <tbody>
-				    <tr><td><code>-output=score_ascii</code></td><td> outputs a TCS evaluation file</td></tr>
-				    <tr><td><code>-output=tcs_residue_filter_N</code></td><td> Removes all <b>residues</b> with a TCS score lower than N</td></tr>
-				    <tr><td><code>-output=tcs_columns_filter_N</code></td><td> Removes all <b>columns</b> with a TCS score lower than N</td></tr>
-				    <tr><td><code>-output=tcs_weighted</code></td><td> Duplicates all columns according to their TCS scoreN, The output is in Phylips</td></tr>
-				    <tr><td><code>-output=tcs_replicate_N</code></td><td> Generates N phylips replicates, with columns drawn according to their TCS score</td></tr>
-				  </tbody>
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-		      <center><h2><font color="#8B4513"><a name="OUTPUT">OUTPUT</a></font></h2></center>
-		      <center><table bgcolor="white">
-			    <tbody>
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-			      <td>
-				<p align="justify">Given an alignment file <a href='BB11001.aln' target='_blank'>BB11001.aln</a>, TCS outputs a file named <code>BB11001.score_html</code> that contains a color coded indicating the agreement between the library and the considered alignment. Red brick regions are in perfect transitive consistant relation between the library and the the input alignment, while blue regions have a very poor agreement.
-				Red brick regions can safely be assumed to be trusted while blue regions should be discarted. Green and Yellow regions should also be used with caution, especially when reconstructing a tree or building a profile. The top of the output provides the average conistency (0-100) for each sequence, thus indicating wether some sequences may have a less reliable alignment. A score lower than 50 should be considered poor.</p>
-				<img border="0" src="F4_scoreHtml.jpg">
-			      </td>
-			    </tr>
-			    <tr>
-			      <td>
-				<p align="justify">Besides .score_html, there are other detailed outputs:				
-				  <ul>
-				    <li> <i>score_ascii</i> : contains ascii format for score_html.
-				    <li> <i>score_pdf</i> : will transfer score_html into pdf format.
-				    <li> <i>sp_ascii</i> : is a format reporting the TCS score of every aligned pair in the target MSA.
-				    <li> <i>tcs_column_filter2</i> : outputs an MSA in which columns having ColumnTCS lower than 2 are removed.
-				    <li> <i>tcs_weighted</i> : outputs an MSA in which columns are duplicated according to their ColumnTCS weight.
-				    <li> <i>tcs_replicate100</i> : outputs 100 replicate MSAs in which columns are randomly drawn according to their weights.
-				</ul>
-			      </td>
-			    </tr>  
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-		    </td>
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-		      <center><h2><font color="#8B4513"><a name="COMMANDS">DOCUMENTATION</a></font></h2></center>
-		      <table bgcolor="white">
-			  <tbody><tr>
-			    <td>
-			      <p>The full documentation is on the <a href="http://www.tcoffee.org/Projects/tcs/index.html#DOCUMENTATION">T-Coffee Homepage</a>. But the following shortcuts may be useful.</p>
-			      <table border="0" width="100%" cellpadding="5" bgcolor="white">
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-		      <center><h2><font color="#8B4513"><a name="LINKS">LINKS</a></font></h2></center>
-		      <table bgcolor="white">
-			  <tbody><tr>
-			    <td>
-			      structural validation
-			      <ul>
-			      <li><a href="http://lbgi.fr/balibase/">BAliBASE 3</a></li>
-			      <li><a href="http://www.drive5.com/bench/">PREFAB 4</a></li>
-			      </ul>
-			      phylogenetic validation
-			      <ul>
-				<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/18218900">yeasts</a> from Wong et al. Science, 2008</li>
-				<li><a href="geneList_YeastToL.txt">subset gene list </a> : at least one aligner yields a phylogeny topology identical to the canonical yeast ToL</li>
-			        <li><a href="http://molevol.cmima.csic.es/castresana/Gblocks.html">tips16</a> from Gblocks</li>
-			        <li><a href="http://trimal.cgenomics.org/">tips32, tips64</a> from trimAl</li>
-			      </ul>
-			    </td>
-			  </tr>
-		      </tbody></table>
-		    </td>
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-		  </tr>
-		  <tr>
-		    <td bgcolor="white" valign="top">
-		      <center><h2><font color="#8B4513"><a name="CONTACT">CONTACT</a></font></h2></center>
-		      <table bgcolor="white">
-			  <tbody><tr>
-			    <td>
-			      <p>Our projects relie on your feeback. Please send me an
-				E-mail if you wish to make a request, a comment, or report a bug! 
-				<code>
-				  <br><br>
-				  *******************************************<br>
-				  Dr. Cedric Notredame, PhD.                 <br>       
-				  Group Leader                               <br>
-				  Comparative Bioinformatics Group           <br>
-				  Bioinformatics and Genomics Programme      <br>
-				  Center for Genomic Regulation (CRG)        <br>
-				  Dr Aiguader, 88                            <br>
-				  08003 Barcelona                            <br>
-				  Spain                                      <br>
-				  Email:  <a href="mailto:cedric.notredame@europe.com">cedric.notredame@europe.com</a>    <br>
-				  HOME :  <a href="http://www.tcoffee.org/">http://www.tcoffee.org/</a><br>
-				  GROUP:  <a href="http://pasteur.crg.es/portal/page/portal/Internet/02_Research/01_Programmes/01_Bioinformatics_Genomics/03_Comparative_Bioinformatics">CRG</a><br>
-				  Phone:  +34 933 160 271                <br>
-				  *******************************************       <br>
-				</code>
-			    </p></td>
-			  </tr>
-		      </tbody></table>
-		    </td>
-		  </tr>
-		  
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-		    <td colspan="5" bgcolor="#FFEBCD"><br></td>
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-		      
-		      <center>
-			<hr>
-				<table width="100%" cellpadding="15" cellspacing="0" cellborder="0" valign="top">
-			    <tbody><tr align="center">
-			      <td width="15%" onmouseover="style.backgroundColor=&#39;white&#39;;" onmouseout="style.backgroundColor=&#39;#FFE4C4&#39;"><b><a href="http://www.tcoffee.org/Projects/homepage.html"><font color="#8B4513">HOME</font></a></b></td>
-			      <td width="15%" onmouseover="style.backgroundColor=&#39;white&#39;;" onmouseout="style.backgroundColor=&#39;#FFE4C4&#39;"><b><a href="http://www.tcoffee.org/Projects/tcs/#SERVERS"><font color="#8B4513">SERVERS</font></a></b></td>
-			      <td width="15%" onmouseover="style.backgroundColor=&#39;white&#39;;" onmouseout="style.backgroundColor=&#39;#FFE4C4&#39;"><b><a href="http://www.tcoffee.org/Projects/tcs/#DOWNLOAD"><font color="#8B4513">DOWNLOAD</font></a></b></td>
-			      <td width="15%" onmouseover="style.backgroundColor=&#39;white&#39;;" onmouseout="style.backgroundColor=&#39;#FFE4C4&#39;"><b><a href="http://www.tcoffee.org/Projects/tcs/#COMMANDS"><font color="#8B4513">DOCUMENTATION</font></a></b></td>
-			      <td width="15%" onmouseover="style.backgroundColor=&#39;white&#39;;" onmouseout="style.backgroundColor=&#39;#FFE4C4&#39;"><b><a href="http://www.tcoffee.org/Projects/tcs/#OUTPUT"><font color="#8B4513">OUTPUT</font></a></b></td>
-			      <td width="15%" onmouseover="style.backgroundColor=&#39;white&#39;;" onmouseout="style.backgroundColor=&#39;#FFE4C4&#39;"><b><a href="http://www.tcoffee.org/Projects/tcs/#CONTACT"><font color="#8B4513">CONTACT</font></a></b></td>
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diff --git a/public_html/Projects/trmsd/index.html b/public_html/Projects/trmsd/index.html
index abd4ff5..308ae9d 100755
--- a/public_html/Projects/trmsd/index.html
+++ b/public_html/Projects/trmsd/index.html
@@ -238,7 +238,7 @@
 				  Dr Aiguader, 88                            <br>
 				  08003 Barcelona                            <br>
 				  Spain                                      <br>
-				  Email:  <A href="MAILTO:cedric.notredame@europe.com">cedric.notredame@europe.com</A>    <br>
+				  Email:  <A href="MAILTO:cedric.notredame@gmail.com">cedric.notredame@gmail.com</A>    <br>
 				  HOME :  <A HREF="http://www.tcoffee.org/homepage.html">http://www.tcoffee.org/homepage.html</A><br>
 				  GROUP:  <a href="http://pasteur.crg.es/portal/page/portal/Internet/02_Research/01_Programmes/01_Bioinformatics_Genomics/03_Comparative_Bioinformatics">CRG</A><br>
 				  Phone:  +34 933 160 271                <br>
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-		      <center><table><tr><td align="center"><b> <FONT size="7" color="#8B4513">T-RMSD <br>A Fine-Grained Structure Clustering Method</font></b></td></tr></table></center>
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-		      <center><h2><FONT color="#8B4513">What is T-RMSD?</FONT></h2></center>
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-			      <P align="justify">T-RMSD (Tree based on Root Mean Square Deviation) is a distance RMSD (dRMSD) based method which generate Structural Trees (analogue to phylogenetic tree) to determine fine-grained structural variations associated with a given Multiple Sequence Alignment (generated by the user using the method of is choice). It is part of the T-Coffee distribution. The specificity of T-RMSD compared to other structural comparison methods stems from its capacity to generate a structural tree with values  equivalent bootstrap values supporting the structural clustering. Such clustering is achieved by the construction of matrixes of distances, calculated between equivalent residues as defined by the ungapped column of the given MSA. The resulting matrixes are then combined using the CONSENSE program from the PHYLIP package to generate a consensus structural tree with equivalent bootstrap values supporting each node(from 0 to 100; 100 indicating that all positions support the clustering).  </P>
-			      <P>A list of related publications is available <a href="http://www.ncbi.nlm.nih.gov/pubmed/20471393,16873492,17032685" target="_blank" >here</a> and the following <a target="_blank" href="./trmsd.ppt">presentation</a> provides an overview of the algorithm and its validation.</p>
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-		      <center><h2><FONT color="#8B4513"><a name="DOWNLOAD">DOWNLOAD</a></font></h2></center>
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-			      <UL>
-				<LI>T-RMSD is a special option allowing a fine-grained structural clustering of a given group of related proteins (i.e. protein domains). 
-				   Download the latest T-Coffee version <a href="../tcoffee/index.html#DOWNLOAD">here</a>.</LI>
-			      </UL>
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-		      <center><h2><FONT color="#8B4513"><a name="INSTALLATION">INSTALLATION</a></font></h2></center>
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-			      <P align="justify"><b>1-</b>Follow the standard T-Coffee <a href="../tcoffee/index.html#INSTALLATION">installation procedure</a>.</P>
-			    </td>
-			  </tr>
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-			      <P align="justify"><b>2-</b>Install all the multiple sequence alignment packages you want to construct your Multiple Sequence Alignment. 
-			      You should also take a look at the <a href="../tcoffee/index.html#DOCUMENTATION">T-Coffee Technical Documentation</a>. The latest list of packages interfaced with T-Coffee can also be obtained with the simple intruction
-			      <code>  t_coffee > <a target="_blank" href="../tcoffee/package_list.txt">package_list</a> </code></P>
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-		      <center><h2><FONT color="#8B4513"><a name="OUTPUT">OUTPUT</a></font></h2></center>
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-				<P align=justify>Given a Multiple Sequence Alignment <code>foo.aln</code> and a template file <code>foo.template_list</code> (similar to Expresso procedure; it corresponds to the association between sequences contained in the MSA and the PDB files used for the distances calculation) T-RMSD outputs a file named <code>foo.html</code> that contains a color coded indication of the ungapped column supporting the structural clustering. Gapped columns are not colored as they are not used to establish the clustering. Red brick columns indicate positions with a strong support to the clustering, while blue regions exhibit a low support. Red brick columns represent the most structurally discriminating positions. Unlike alginments generated using T-Coffee, there is no consistency score (0-100) for each sequence of the MSA. T-RMSD also outputs several files named <code>foo.struc_tree10, foo.struc_tree50, foo.struc_tree100</code> which corresponding to Neighbour Joining files, that can be used to build the structural tree using the software of your choice. The indication 10, 50 or 100 represent the pourcentage of ungapped columns used to generate the clustering.  </P>
-				<a href="CRD_tree.png" target="_blank" title="Click to zoom"><img border="0" src="CRD_tree.png" width="350" height="350" ></a>
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-		      <center><h2><FONT color="#8B4513"><a name="COMMANDS">DOCUMENTATION</a></font></h2></center>
-		      <table bgcolor="white">
-			  <tr>
-			    <td>
-			      <p>The full documentation is on the <a href="../tcoffee/index.html#DOCUMENTATION">T-Coffee Homepage</a>. But the following shortcuts may be useful.</p>
-			      <TABLE border=0 WIDTH="100%" CELLPADDING="5" bgcolor="white">
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-				    <TD>To run a T-RMSD from a given MSA, type</td>
-				  </TR>
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-				    <td>
-				      <code>t_coffee -other_pg trmsd <i>foo.aln</i> -template file <i>foo.template_list</i> -mode msa2tree</code>
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-		      <center><h2><FONT color="#8B4513"><a name="LINKS">LINKS</a></font></h2></center>
-		      <table bgcolor="white">
-			  <tr>
-			    <td>
-			      <LI><A HREF="http://ekhidna.biocenter.helsinki.fi/dali_server/">Dali server</A> Dali server v3.0 </LI>
-			    </td>
-			  </tr>
-			  <tr>
-			    <td>
-			      <LI><A HREF="http://www.cathdb.info/index.html">CATH database</A> CATH homepage v3.3 </LI>
-			    </td>
-			  </tr>
-			  <tr>
-			    <td>
-			      <LI><A HREF="http://scop.mrc-lmb.cam.ac.uk/scop/">SCOP server</A> SCOP homepage 1.75 release </LI>
-			    </td>
-			  </tr>	  
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-		      <center><h2><FONT color="#8B4513"><a name="CONTACT">CONTACT</a></font></h2></center>
-		      <table bgcolor="white">
-			  <tr>
-			    <td>
-			      <P>Our projects relie on your feeback. Please send me an
-				E-mail if you wish to make a request, a comment, or report a bug! 
-				<code>
-				  <br><br>
-				  *******************************************<br>
-				  Dr. Cedric Notredame, PhD.                 <br>       
-				  Group Leader                               <br>
-				  Comparative Bioinformatics Group           <br>
-				  Bioinformatics and Genomics Programme      <br>
-				  Center for Genomic Regulation (CRG)        <br>
-				  Dr Aiguader, 88                            <br>
-				  08003 Barcelona                            <br>
-				  Spain                                      <br>
-				  Email:  <A href="MAILTO:cedric.notredame@europe.com">cedric.notredame@europe.com</A>    <br>
-				  HOME :  <A HREF="http://www.tcoffee.org/homepage.html">http://www.tcoffee.org/homepage.html</A><br>
-				  GROUP:  <a href="http://pasteur.crg.es/portal/page/portal/Internet/02_Research/01_Programmes/01_Bioinformatics_Genomics/03_Comparative_Bioinformatics">CRG</A><br>
-				  Phone:  +34 933 160 271                <br>
-				  *******************************************       <br>
-				</code>
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diff --git a/public_html/Publications/Pdf/all.txt b/public_html/Publications/Pdf/all.txt
index 69316f3..4dbda1b 100755
--- a/public_html/Publications/Pdf/all.txt
+++ b/public_html/Publications/Pdf/all.txt
@@ -20,7 +20,7 @@ Keywords: multiple alignment; structural superposition; TCoffee; threading; sap
 
 Introduction
 It has long been assumed that using structural information can increase the accuracy of multiple protein sequence alignments (MSA).1 Recent results2,3 suggest that accurate MSAs obtained this way are useful for making functional assignments. These �ndings are quite exciting in a context where a structure may soon be available for each protein family (transmembrane proteins excepted).4 However, making the best out of this wealth of data will require the development of new automatic methods, able to ef�ciently incorporate protein structure information within
-Abbreviations used: MSA, multiple protein sequence alignment(s); S-MSA, structure-based MSA; DP, dynamic programming; NW, Needlman & Wunsch; CS, column score. E-mail address of the corresponding author: cedric.notredame@europe.com
+Abbreviations used: MSA, multiple protein sequence alignment(s); S-MSA, structure-based MSA; DP, dynamic programming; NW, Needlman & Wunsch; CS, column score. E-mail address of the corresponding author: cedric.notredame@gmail.com
 
 MSAs. The incentive for doing so is very strong, considering the critical role MSAs play in so many sequence analysis applications,5 like phylogenetic reconstruction, structure prediction, functional characterization, database searches and nonsynonymous single nucleotide polymorphism characterization.6 Despite their usefulness, accurate MSAs remain dif�cult to compute, owing to reasons that are both computational7 and biological.8 From a computational point of view, the assembly of an optimal MSA is a complex problem and an exact solution can be computed only for small sets of related sequences.9 This is the reason why most packages use an approximate heuristic, the progressive alignment algorithm,10 that gives no guarantee on delivering an optimal solution but can rapidly align large sets of sequences. On the biological side, one is limited by the lack of an objective and accurate criterion to assess MSA quality.8 As a consequence, most methods use
 
@@ -154,7 +154,7 @@ INTRODUCTION The assembly of an accurate multiple sequence alignment (MSA) is a
 
 they deliver alignments that are only partly correct from a structural point of view (8), thus suggesting that sequencebased alignment procedures can still be greatly improved. In the current situation, the best way to produce a high-quality MSA remains the assembly of a multiple structural alignment. Unfortunately, few examples exist where enough related structures are available to carry out such a task. An elegant alternative to the use of many structures is to mix sequences and structures, in the hope that the 3D information contained within the structures will help deliver a better alignment of the other sequences. Such a mix also constitutes a realistic solution, considering the increasing proportion of sequences without a known structure and the decreasing proportion of protein families not associated with at least one structure. However, the problem of combining sequences and structures has not yet been extensively addressed, and only a handful of methods are available that allow the seamless combining of sequences and structures (9) while appropriately using 3D information. Here we present 3DCoffee@igs, a web server especially designed to combine sequences and structures by seamlessly integrating in T-Coffee (10) the three types of alignment methods needed for this purpose: sequence–sequence, sequence–structure and structure–structure alignment methods. When using one or more structures, the alignments thus produced are more accurate than similar alignments based on sequence information alone, as judged by the comparison with reference structure-based alignments (O.O’Sullivan, K.Suhre, D.Higgins and C.Notredame, submitted for publication). The inclusion of a threading method (sequence– structure alignment) makes it possible to use as little as one structure. METHODS Standard T-Coffee sequence alignment assembly We use T-Coffee to mix sequences and structures. Given a set of sequences, the regular T-Coffee procedure involves the
 
-*To whom correspondence should be addressed. Tel: +33 491 164 606; Fax: +33 491 164 549; Email: cedric.notredame@europe.com The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. ª 2004, the authors
+*To whom correspondence should be addressed. Tel: +33 491 164 606; Fax: +33 491 164 549; Email: cedric.notredame@gmail.com The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. ª 2004, the authors
 
 Nucleic Acids Research, Vol. 32, Web Server issue ª Oxford University Press 2004; all rights reserved
 
@@ -201,7 +201,7 @@ Received on January 6, 2000; revised on Month xx, 2000; accepted on February 20,
 
 Author please check use of A and B heads is correct
 
-ABSTRACT Motivation: We describe APDB, a novel measure for evaluating the quality of a protein sequence alignment, given two or more PDB structures. This evaluation does not require a reference alignment or a structure superposition. APDB is designed to ef�ciently and objectively benchmark multiple sequence alignment methods. Results: Using existing collections of reference multiple sequence alignments and existing alignment methods, we show that APDB gives results that are consistent with those obtained using conventional evaluations. We also show that APDB is suitable for evaluating sequence alignments that are structurally equivalent. We conclude that APDB provides an alternative to more conventional methods used for benchmarking sequence alignment packages. Availability: APDB is implemented in C, its source code and its documentation are available for free on request from the authors. Contact: cedric.notredame@europe.com
+ABSTRACT Motivation: We describe APDB, a novel measure for evaluating the quality of a protein sequence alignment, given two or more PDB structures. This evaluation does not require a reference alignment or a structure superposition. APDB is designed to ef�ciently and objectively benchmark multiple sequence alignment methods. Results: Using existing collections of reference multiple sequence alignments and existing alignment methods, we show that APDB gives results that are consistent with those obtained using conventional evaluations. We also show that APDB is suitable for evaluating sequence alignments that are structurally equivalent. We conclude that APDB provides an alternative to more conventional methods used for benchmarking sequence alignment packages. Availability: APDB is implemented in C, its source code and its documentation are available for free on request from the authors. Contact: cedric.notredame@gmail.com
 
 INTRODUCTION We introduce APDB (Analyze alignments with PDB), a new method for benchmarking and improving multiple sequence alignment packages with minimal human intervention. We show how it is possible to avoid the use of reference alignments when PDB structures are available for at least two homologous sequences in a test alignment. Using this method it should become possible to systematically benchmark or train multiple sequence alignment methods using all known structures, in a completely automatic manner. There are strong justi�cations for improving multiple sequence alignment methods. Many sequence analysis
 ∗ To whom correspondence should be addressed.
@@ -346,7 +346,7 @@ APDB: a web server to evaluate the accuracy of sequence alignments using structu
 
 CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM), Parc Scienti�que de Luminy, 163 Avenue de Luminy, FR-13288, Marseille cedex 09, France, 2The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland and 3Institut Suisse de Recherche et d’Experimentation sur le Cancer, Ch. des Boveresses 155 CH-1066 Epalinges, Switzerland
 
-Received on March 31, 2006; revised on June 17, 2006; accepted on July 21, 2006 Associate Editor: Thomas Lengauer ABSTRACT Summary: The APDB webserver uses structural information to evaluate the alignment of sequences with known structures. It returns a score correlated to the overall alignment accuracy as well as a local evaluation. Any sequence alignment can be analyzed with APDB provided it includes at least two proteins with known structures. Sequences without a known structure are simply ignored and do not contribute to the scoring procedure. Availability: APDB is part of the T-Coffee suite of tools for alignment analysis, it is available on www.tcoffee.org. A standalone version of the package is also available as a freeware open source from the same address. Contact: cedric.notredame@europe.com
+Received on March 31, 2006; revised on June 17, 2006; accepted on July 21, 2006 Associate Editor: Thomas Lengauer ABSTRACT Summary: The APDB webserver uses structural information to evaluate the alignment of sequences with known structures. It returns a score correlated to the overall alignment accuracy as well as a local evaluation. Any sequence alignment can be analyzed with APDB provided it includes at least two proteins with known structures. Sequences without a known structure are simply ignored and do not contribute to the scoring procedure. Availability: APDB is part of the T-Coffee suite of tools for alignment analysis, it is available on www.tcoffee.org. A standalone version of the package is also available as a freeware open source from the same address. Contact: cedric.notredame@gmail.com
 
 1
 
@@ -707,7 +707,7 @@ The iRMSD: a local measure of sequence alignment accuracy using structural infor
 ´ Laboratoire Information Genomique et Structurale, CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM), Parc Scienti�que de Luminy, case 934, 163 Avenue de Luminy, FR-13288, Marseille cedex 09
 ture based alignments as unambiguous and unquestionable gold standards, a closer look reveals a much less clear cut situation. More than 20 structure alignment packages have been developed (Goldsmith-Fischman and Honig, 2003). All these packages tend to produce different alignments because of their different underlying optimization algorithms. Furthermore, the lack of a universally accepted criterion for describing the quality of a structural alignment makes it dif�cult to determine the relative merits of all these packages (Kolodny, et al., 2005). The most common procedure to evaluate structure superpositions is to use the root mean square distance deviation (RMSD) of superposed atoms. This measure estimates the mean square distance between the equivalent alpha carbons of the two superposed structures. It can be ambiguous because of its dependence on two critical parameters: the minimization method and the procedure used to exclude structurally non equivalent regions (loops for instance). Having several methods that deliver structure based sequence alignments and not knowing which one does best is a major issue in a context where structure-based alignments are routinely used to improve and guide the development of sequence alignment methods (Wallace, et al., 2005). A direct consequence of this situation has been the development of at least �ve collections of reference structure based sequence alignments (Edgar, 2004; Mizuguchi, et al., 1998; O’Sullivan, et al., 2004; Raghava, et al., 2003; Thompson, et al., 2005; Van Walle, et al., 2005). These collections are all used for a similar purpose: the benchmark of sequence alignment algorithms. Since it is virtually impossible to compare these datasets and decide whether some are more informative than others, the most common practice is to use them all, and look for common trends in the global results (Katoh, et al., 2005). While results measured on these reference collections tend to agree for datasets with more than 30% identity, variations appear when considering sets of remote homologues (Katoh, et al., 2005). Aside from potential accuracy problems, the simplest explanation for these discrepancies is the possibility for alternative sequence alignments to be structurally equivalent, especially when considering remote homologues (Lackner, et al., 2000). In this context, setting one speci�c alignment as a reference becomes an arbitrary choice and therefore a bias toward speci�c alignment methods. In practice, the authors try to minimize that effect by specifying the core regions that should be used for the comparison, but this choice is also dif�cult and somehow arbitrary. We suggest in this paper that replacing the reference alignments with an RMSD measure would
 
-ABSTRACT Motivation: We introduce the iRMSD, a new type of RMSD, independent from any structure superposition and suitable for evaluating sequence alignments of proteins with known structures. Results: We demonstrate that the iRMSD is equivalent to the standard RMSD although much simpler to compute and we also show that it is suitable for comparing sequence alignments and benchmarking multiple sequence alignment methods. We tested the iRMSD score on 6 established multiple sequence alignment packages and found the results to be consistent with those obtained using an established reference alignment collection like Prefab. Availability: The iRMSD is part of the T-Coffee package and is distributed as an open source freeware (http://www.tcoffee.org/). Contact: cedric.notredame@europe.com; cedric.notredame@igs. cnrs-mrs.fr
+ABSTRACT Motivation: We introduce the iRMSD, a new type of RMSD, independent from any structure superposition and suitable for evaluating sequence alignments of proteins with known structures. Results: We demonstrate that the iRMSD is equivalent to the standard RMSD although much simpler to compute and we also show that it is suitable for comparing sequence alignments and benchmarking multiple sequence alignment methods. We tested the iRMSD score on 6 established multiple sequence alignment packages and found the results to be consistent with those obtained using an established reference alignment collection like Prefab. Availability: The iRMSD is part of the T-Coffee package and is distributed as an open source freeware (http://www.tcoffee.org/). Contact: cedric.notredame@gmail.com; cedric.notredame@igs. cnrs-mrs.fr
 
 1
 
@@ -849,7 +849,7 @@ Mocca: semi-automatic method for domain hunting
 Information Genetique et Structurale, CNRS-UMR 1889, 31 Ch. Joseph Aiguier, 13 402 Marseille, France
 Received on Month xx, 2000; revised and accepted on Month xx, 2000
 
-ABSTRACT Motivation: Multiple OCCurrences Analysis (Mocca) is a new method for repeat extraction. It is based on the TCoffee package (Notredame et al., JMB, 302, 205–217, 2000). Given a sequence or a set of sequences, and a library of local alignments, Mocca extracts every segment of sequence homologous to a pre-speci�ed master. The Q: implementation is meant for domain hunting and makes Please it fast and easy to test for new boundaries or extend known supply recevied repeats in an interactive manner. Mocca is designed to date Q: deal with highly divergent protein repeats (less than 30% Applications amino acid identity) of more than 30 amino acids. Note? Q: Availability: Mocca is available on request (cedric. There are some notredame@europe.com). The software is free of charge differences in the and comes along with complete documentation.
+ABSTRACT Motivation: Multiple OCCurrences Analysis (Mocca) is a new method for repeat extraction. It is based on the TCoffee package (Notredame et al., JMB, 302, 205–217, 2000). Given a sequence or a set of sequences, and a library of local alignments, Mocca extracts every segment of sequence homologous to a pre-speci�ed master. The Q: implementation is meant for domain hunting and makes Please it fast and easy to test for new boundaries or extend known supply recevied repeats in an interactive manner. Mocca is designed to date Q: deal with highly divergent protein repeats (less than 30% Applications amino acid identity) of more than 30 amino acids. Note? Q: Availability: Mocca is available on request (cedric. There are some notredame@gmail.com). The software is free of charge differences in the and comes along with complete documentation.
 electronic version and hardcopy. We follow electronic version
 
 information concerning the whereabouts of one of the repeats (master repeat), it allows the user to tune the parameters describing the repeat family (i.e. start position, length of the master repeat and stringency of the search), and extract other occurrences of that repeat within the dataset. The procedure is fast and simple.
@@ -869,7 +869,7 @@ Fig. 1. Layout of the Mocca strategy. The main steps required to extract a repea
 ACKNOWLEDGEMENTS The author wishes to thank the following people: Des Higgins for very helpful comments. Jaap Heringa, Philipp Bucher and Kay Hoffmann for useful discussions and advice at an early stage of the project, Hiroyuki Ogata for helpful comments on the program. REFERENCES
 Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D. (1997) Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389–3402. Bairoch,A., Bucher,P. and Hofmann,K. (1997) The PROSITE database, its status in 1997. Nucleic Acids Res., 25, 217–221. Chothia,C. (1992) Proteins: 1000 families for the molecular biologist. Nature, 357, 543–544. Corpet,F., Gouzy,J. and Kahn,D. (1998) The ProDom database of protein domain families. Nucleic Acids Res., 26, 323–326. Durbin,R., Eddy,S., Krogh,A. and Mitchinson,G. (1998) Biological Sequence Analysis. 1 vols, Cambridge University Press, Cambridge. Heger,A. and Holm,L. (2000) Rapid automatic detection and alignment of repeats in protein sequences. Proteins, 41, 224–237. Heringa,J. and Argos,P. (1993) A method to recognise distant repeats in protein sequences. Proteins: Struct. Funct. Genet., 17, 391–411. Holm,L. and Sander,C. (1998) Dictionary of recurrent domains in protein structures. Proteins, 33, 88–96.
 
-makes it possible for a single repeat to ‘recognize’ each of its homologues (even the distant ones). The extraction process relies on a very ef�cient dynamic programming procedure known as repeated matches (Durbin et al., 1998). This algorithm reports a series of non-overlapping sub-strings each of them having an alignment to the master associated with a score higher than some pre-speci�ed threshold T h. T h is empirically set to be a function of the maser repeat length (L): Th = S ∗ L S has a value between 0 and 1. By default, S = 0.05, but its value can be modi�ed interactively. Two other parameters can also be modi�ed to increase sensitivity and accuracy: the gap opening penalty and the gap extension. Mocca is part of the T-Coffee package. It is written in Perl and ANSI C. It runs on any UNIX or LINUX platform. It is available free of charge along with documentation. Copies can be obtained on request by sending an e-mail to cedric.notredame@europe.com. The main com2
+makes it possible for a single repeat to ‘recognize’ each of its homologues (even the distant ones). The extraction process relies on a very ef�cient dynamic programming procedure known as repeated matches (Durbin et al., 1998). This algorithm reports a series of non-overlapping sub-strings each of them having an alignment to the master associated with a score higher than some pre-speci�ed threshold T h. T h is empirically set to be a function of the maser repeat length (L): Th = S ∗ L S has a value between 0 and 1. By default, S = 0.05, but its value can be modi�ed interactively. Two other parameters can also be modi�ed to increase sensitivity and accuracy: the gap opening penalty and the gap extension. Mocca is part of the T-Coffee package. It is written in Perl and ANSI C. It runs on any UNIX or LINUX platform. It is available free of charge along with documentation. Copies can be obtained on request by sending an e-mail to cedric.notredame@gmail.com. The main com2
 
 Mocca and domain hunting
 
@@ -2689,7 +2689,7 @@ Keywords: multiple alignment; structural superposition; TCoffee; threading; sap
 
 Introduction
 It has long been assumed that using structural information can increase the accuracy of multiple protein sequence alignments (MSA).1 Recent results2,3 suggest that accurate MSAs obtained this way are useful for making functional assignments. These �ndings are quite exciting in a context where a structure may soon be available for each protein family (transmembrane proteins excepted).4 However, making the best out of this wealth of data will require the development of new automatic methods, able to ef�ciently incorporate protein structure information within
-Abbreviations used: MSA, multiple protein sequence alignment(s); S-MSA, structure-based MSA; DP, dynamic programming; NW, Needlman & Wunsch; CS, column score. E-mail address of the corresponding author: cedric.notredame@europe.com
+Abbreviations used: MSA, multiple protein sequence alignment(s); S-MSA, structure-based MSA; DP, dynamic programming; NW, Needlman & Wunsch; CS, column score. E-mail address of the corresponding author: cedric.notredame@gmail.com
 
 MSAs. The incentive for doing so is very strong, considering the critical role MSAs play in so many sequence analysis applications,5 like phylogenetic reconstruction, structure prediction, functional characterization, database searches and nonsynonymous single nucleotide polymorphism characterization.6 Despite their usefulness, accurate MSAs remain dif�cult to compute, owing to reasons that are both computational7 and biological.8 From a computational point of view, the assembly of an optimal MSA is a complex problem and an exact solution can be computed only for small sets of related sequences.9 This is the reason why most packages use an approximate heuristic, the progressive alignment algorithm,10 that gives no guarantee on delivering an optimal solution but can rapidly align large sets of sequences. On the biological side, one is limited by the lack of an objective and accurate criterion to assess MSA quality.8 As a consequence, most methods use
 
@@ -2982,7 +2982,7 @@ INTRODUCTION The assembly of an accurate multiple sequence alignment (MSA) is a
 
 they deliver alignments that are only partly correct from a structural point of view (8), thus suggesting that sequencebased alignment procedures can still be greatly improved. In the current situation, the best way to produce a high-quality MSA remains the assembly of a multiple structural alignment. Unfortunately, few examples exist where enough related structures are available to carry out such a task. An elegant alternative to the use of many structures is to mix sequences and structures, in the hope that the 3D information contained within the structures will help deliver a better alignment of the other sequences. Such a mix also constitutes a realistic solution, considering the increasing proportion of sequences without a known structure and the decreasing proportion of protein families not associated with at least one structure. However, the problem of combining sequences and structures has not yet been extensively addressed, and only a handful of methods are available that allow the seamless combining of sequences and structures (9) while appropriately using 3D information. Here we present 3DCoffee@igs, a web server especially designed to combine sequences and structures by seamlessly integrating in T-Coffee (10) the three types of alignment methods needed for this purpose: sequence–sequence, sequence–structure and structure–structure alignment methods. When using one or more structures, the alignments thus produced are more accurate than similar alignments based on sequence information alone, as judged by the comparison with reference structure-based alignments (O.O’Sullivan, K.Suhre, D.Higgins and C.Notredame, submitted for publication). The inclusion of a threading method (sequence– structure alignment) makes it possible to use as little as one structure. METHODS Standard T-Coffee sequence alignment assembly We use T-Coffee to mix sequences and structures. Given a set of sequences, the regular T-Coffee procedure involves the
 
-*To whom correspondence should be addressed. Tel: +33 491 164 606; Fax: +33 491 164 549; Email: cedric.notredame@europe.com The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. ª 2004, the authors
+*To whom correspondence should be addressed. Tel: +33 491 164 606; Fax: +33 491 164 549; Email: cedric.notredame@gmail.com The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. ª 2004, the authors
 
 Nucleic Acids Research, Vol. 32, Web Server issue ª Oxford University Press 2004; all rights reserved
 
@@ -3029,7 +3029,7 @@ INTRODUCTION The multiple alignment of DNA or protein sequences is one of the mo
 
 Unfortunately the standard multiple sequence alignment problem is NP-hard, which means that it is impossible to solve it for more than a few sequences. This complexity explains why so many different approaches have been developed (1,2), such as progressive alignment (3), iteration (4–6) and genetic algorithms (7). One very useful development has been the design of consistency-based methods whose purpose is to generate an alignment consistent with a set of pairwise alignments. The use of consistency was �rst described by Gotoh (8) and Kececioglu (9) and independently re-formalized by Vingron and Argos (10) as a dot matrix multiplication procedure that bears much resemblance with T-Coffee. Consistency was later re-discovered by Morgenstern et al. (11) who refers to it as overlapping weights. In 2000, Notredame et al. (12) described a novel algorithm combining the overlapping weights with a progressive alignment strategy. This algorithm was implemented in T-Coffee and resulted in signi�cant accuracy improvement over existing methods. Since then, consistency based objective functions have been used within several new multiple alignment packages, including POA (13), MAFFT 5 (14), Muscle 6 (5), ProbCons (15) and PCMA (16). More than 50 MSA methods have been described over the last 10 years (Medline, January 08, 2006), with no less than 20 new publications in 2005 alone. The complexity and variety of these algorithms and the fact than none provides a de�nite answer to the problem makes it almost impossible to tell them apart from a theoretical point of view. In practice however, these methods are compared using empirical evaluations made on structure-based sequence alignments. This popular approach suffers from at least two shortcomings, most notably the fact that MSA methods trained and evaluated this way are biased toward generating structurally rather than evolutionarily correct alignments. Furthermore, although structural information is more resilient than sequence signal over long evolutionary distances, the assembly of a structure-based MSA is in itself a dif�cult task, which has resulted in the
 
-*To whom correspondence should be addressed. Tel: +33 491 825 427; Fax: +33 491 825 420; Email: cedric.notredame@europe.com The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors Ó The Author 2006. Published by Oxford University Press. All rights reserved. The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org
+*To whom correspondence should be addressed. Tel: +33 491 825 427; Fax: +33 491 825 420; Email: cedric.notredame@gmail.com The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors Ó The Author 2006. Published by Oxford University Press. All rights reserved. The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org
 
 Nucleic Acids Research, 2006, Vol. 34, No. 6
 
@@ -3293,7 +3293,7 @@ INTRODUCTION Over the past years, multiple sequence alignments (MSAs) have becom
 
 Unfortunately, MSA packages are not yet accurate enough to deliver all their promises and the sharp increase in the number of methods recently published (25 novel programs over the last 5 years) illustrates well the expectation for improvement within the community. MSAs are not always good enough for large-scale analysis and while immense progress has been made to accurately align multiple sets of sequences with >40% average identity, recent benchmarks published with the MAFFT 5 package (1) reveal that state of the art methods still fail to reliably align distantly related sequences. In the so-called ‘Twilight zone’ (2), sequences with <20% identity cannot be aligned with >30% average accuracy (as judged by comparison with reference alignments). So far, the most convincing solution to this problem has been to supplement sequences with structural information (3). The reason why structure-based MSAs are more accurate is not so much a consequence of better algorithms but rather an effect of structures evolutionary stability. Structures evolve slower than the sequences (4) and even when sequences have diverged beyond recognition it is often possible to establish homology (i.e. common ancestry) on the basis of 3D folds comparisons (3). The increasing availability of structural data (5) means that relying on structure-based methods for sequence analysis has become much more realistic than it used to be. However, sequences are still being determined much faster than structures, thus creating a context where methods able to ef�ciently combine sequences and structure into accurate MSAs are needed. To the best of our knowledge, only six algorithms have been designed that are able to make use of secondary (6,7) or tertiary (8–10) structure information. In the context of this work, we used 3D-Coffee (11) for its ability to combine the output of several methods into one unique model. 3D-Coffee is based on the T-Coffee algorithm (12), a heuristic method that uses a progressive algorithm to compute an MSA having a high consistency with a collection of pre-computed pairwise alignments (the library).
 
-*To whom correspondence should be addressed. Tel: +33 491 825 427; Fax: +33 491 825 420; Email: cedric.notredame@europe.com Ó The Author 2006. Published by Oxford University Press. All rights reserved. The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org
+*To whom correspondence should be addressed. Tel: +33 491 825 427; Fax: +33 491 825 420; Email: cedric.notredame@gmail.com Ó The Author 2006. Published by Oxford University Press. All rights reserved. The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org
 
 Nucleic Acids Research, 2006, Vol. 34, Web Server issue
 
@@ -3354,7 +3354,7 @@ A
 
 substitution matrix during a regular progressive alignment. The aim is to deliver a �nal MSA as consistent as possible with the alignments contained in the library. Many recent packages have built upon this initial framework. For instance, PCMA [15] decreases T-Coffee computational requirements by prealigning closely related sequences. ProbCons [7] uses Bayesian consistency and �lls the primary library using the posterior decoding of a pair hidden Markov model. The substitution costs are estimated from this library using Bayesian statistics. MUMMALS [17] combines the ProbCons scoring scheme with the PCMA strategy, while including secondary structure predictions in its pair hidden Markov model. The most accurate flavors of MAFFT [8] (i.e., the GNS and LNS modes) use a T-Coffee–like evaluation. A majority of studies indicate that consistency-based methods are more accurate than their matrix-based counterparts [4], although they typically require an amount of CPU time N times higher than simpler methods (N being the number of sequences). Most of these methods are available online, either as downloadable packages or as online Web services (Table 1). The wealth of available methods and their increasingly similar accuracies makes it harder than ever to objectively choose one over the others. Consensus methods such as MCoffee [12] provide an interesting framework to address this problem. M-Coffee is a consensus meta-method based on TCoffee. Given a sequence dataset, it �lls up the library by using various MSA methods to compute alternative alignments. T-Coffee then uses this library to compute a �nal MSA consistent with the original alignments. When combining eight of the most accurate and distinct MSA packages, M-Coffee produces 67% of the time a better MSA than ProbCons, the best individual method [12]. Aside from its ease of extension, M-Coffee’s main advantage is its ability to estimate the local consistency between the �nal alignment and the combined MSAs (CORE index [21]; Figure 1). This useful index has been shown to be well-correlated with the MSAs’ structural correctness [21,22]. M-Coffee is not, however, the ultimate answer to the MSA problem, and its limited performances on remote homologs suggest that
 
-Editor: Fran Lewitter, Whitehead Institute, United States of America Citation: Notredame C (2007) Recent evolutions of multiple sequence alignment algorithms. PLoS Comput Biol 3(8): e123. doi:10.1371/journal.pcbi.0030123 ´dric Notredame. This is an open-access article distributed Copyright: Ó 2007 Ce under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Abbreviations: MSA, multiple sequence alignment ´ ´nomique et Structurale, CNRS UPR2589, Cedric Notredame is with Information Ge Institute for Structural Biology and Microbiology, Parc Scientifique de Luminy, Marseille, France. E-mail: cedric.notredame@europe.com
+Editor: Fran Lewitter, Whitehead Institute, United States of America Citation: Notredame C (2007) Recent evolutions of multiple sequence alignment algorithms. PLoS Comput Biol 3(8): e123. doi:10.1371/journal.pcbi.0030123 ´dric Notredame. This is an open-access article distributed Copyright: Ó 2007 Ce under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Abbreviations: MSA, multiple sequence alignment ´ ´nomique et Structurale, CNRS UPR2589, Cedric Notredame is with Information Ge Institute for Structural Biology and Microbiology, Parc Scientifique de Luminy, Marseille, France. E-mail: cedric.notredame@gmail.com
 
 PLoS Computational Biology | www.ploscompbiol.org
 
@@ -4425,7 +4425,7 @@ Received on January 6, 2000; revised on Month xx, 2000; accepted on February 20,
 
 Author please check use of A and B heads is correct
 
-ABSTRACT Motivation: We describe APDB, a novel measure for evaluating the quality of a protein sequence alignment, given two or more PDB structures. This evaluation does not require a reference alignment or a structure superposition. APDB is designed to ef�ciently and objectively benchmark multiple sequence alignment methods. Results: Using existing collections of reference multiple sequence alignments and existing alignment methods, we show that APDB gives results that are consistent with those obtained using conventional evaluations. We also show that APDB is suitable for evaluating sequence alignments that are structurally equivalent. We conclude that APDB provides an alternative to more conventional methods used for benchmarking sequence alignment packages. Availability: APDB is implemented in C, its source code and its documentation are available for free on request from the authors. Contact: cedric.notredame@europe.com
+ABSTRACT Motivation: We describe APDB, a novel measure for evaluating the quality of a protein sequence alignment, given two or more PDB structures. This evaluation does not require a reference alignment or a structure superposition. APDB is designed to ef�ciently and objectively benchmark multiple sequence alignment methods. Results: Using existing collections of reference multiple sequence alignments and existing alignment methods, we show that APDB gives results that are consistent with those obtained using conventional evaluations. We also show that APDB is suitable for evaluating sequence alignments that are structurally equivalent. We conclude that APDB provides an alternative to more conventional methods used for benchmarking sequence alignment packages. Availability: APDB is implemented in C, its source code and its documentation are available for free on request from the authors. Contact: cedric.notredame@gmail.com
 
 INTRODUCTION We introduce APDB (Analyze alignments with PDB), a new method for benchmarking and improving multiple sequence alignment packages with minimal human intervention. We show how it is possible to avoid the use of reference alignments when PDB structures are available for at least two homologous sequences in a test alignment. Using this method it should become possible to systematically benchmark or train multiple sequence alignment methods using all known structures, in a completely automatic manner. There are strong justi�cations for improving multiple sequence alignment methods. Many sequence analysis
 ∗ To whom correspondence should be addressed.
@@ -6383,7 +6383,7 @@ Mocca: semi-automatic method for domain hunting
 Information Genetique et Structurale, CNRS-UMR 1889, 31 Ch. Joseph Aiguier, 13 402 Marseille, France
 Received on Month xx, 2000; revised and accepted on Month xx, 2000
 
-ABSTRACT Motivation: Multiple OCCurrences Analysis (Mocca) is a new method for repeat extraction. It is based on the TCoffee package (Notredame et al., JMB, 302, 205–217, 2000). Given a sequence or a set of sequences, and a library of local alignments, Mocca extracts every segment of sequence homologous to a pre-speci�ed master. The Q: implementation is meant for domain hunting and makes Please it fast and easy to test for new boundaries or extend known supply recevied repeats in an interactive manner. Mocca is designed to date Q: deal with highly divergent protein repeats (less than 30% Applications amino acid identity) of more than 30 amino acids. Note? Q: Availability: Mocca is available on request (cedric. There are some notredame@europe.com). The software is free of charge differences in the and comes along with complete documentation.
+ABSTRACT Motivation: Multiple OCCurrences Analysis (Mocca) is a new method for repeat extraction. It is based on the TCoffee package (Notredame et al., JMB, 302, 205–217, 2000). Given a sequence or a set of sequences, and a library of local alignments, Mocca extracts every segment of sequence homologous to a pre-speci�ed master. The Q: implementation is meant for domain hunting and makes Please it fast and easy to test for new boundaries or extend known supply recevied repeats in an interactive manner. Mocca is designed to date Q: deal with highly divergent protein repeats (less than 30% Applications amino acid identity) of more than 30 amino acids. Note? Q: Availability: Mocca is available on request (cedric. There are some notredame@gmail.com). The software is free of charge differences in the and comes along with complete documentation.
 electronic version and hardcopy. We follow electronic version
 
 information concerning the whereabouts of one of the repeats (master repeat), it allows the user to tune the parameters describing the repeat family (i.e. start position, length of the master repeat and stringency of the search), and extract other occurrences of that repeat within the dataset. The procedure is fast and simple.
@@ -6403,7 +6403,7 @@ Fig. 1. Layout of the Mocca strategy. The main steps required to extract a repea
 ACKNOWLEDGEMENTS The author wishes to thank the following people: Des Higgins for very helpful comments. Jaap Heringa, Philipp Bucher and Kay Hoffmann for useful discussions and advice at an early stage of the project, Hiroyuki Ogata for helpful comments on the program. REFERENCES
 Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D. (1997) Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389–3402. Bairoch,A., Bucher,P. and Hofmann,K. (1997) The PROSITE database, its status in 1997. Nucleic Acids Res., 25, 217–221. Chothia,C. (1992) Proteins: 1000 families for the molecular biologist. Nature, 357, 543–544. Corpet,F., Gouzy,J. and Kahn,D. (1998) The ProDom database of protein domain families. Nucleic Acids Res., 26, 323–326. Durbin,R., Eddy,S., Krogh,A. and Mitchinson,G. (1998) Biological Sequence Analysis. 1 vols, Cambridge University Press, Cambridge. Heger,A. and Holm,L. (2000) Rapid automatic detection and alignment of repeats in protein sequences. Proteins, 41, 224–237. Heringa,J. and Argos,P. (1993) A method to recognise distant repeats in protein sequences. Proteins: Struct. Funct. Genet., 17, 391–411. Holm,L. and Sander,C. (1998) Dictionary of recurrent domains in protein structures. Proteins, 33, 88–96.
 
-makes it possible for a single repeat to ‘recognize’ each of its homologues (even the distant ones). The extraction process relies on a very ef�cient dynamic programming procedure known as repeated matches (Durbin et al., 1998). This algorithm reports a series of non-overlapping sub-strings each of them having an alignment to the master associated with a score higher than some pre-speci�ed threshold T h. T h is empirically set to be a function of the maser repeat length (L): Th = S ∗ L S has a value between 0 and 1. By default, S = 0.05, but its value can be modi�ed interactively. Two other parameters can also be modi�ed to increase sensitivity and accuracy: the gap opening penalty and the gap extension. Mocca is part of the T-Coffee package. It is written in Perl and ANSI C. It runs on any UNIX or LINUX platform. It is available free of charge along with documentation. Copies can be obtained on request by sending an e-mail to cedric.notredame@europe.com. The main com2
+makes it possible for a single repeat to ‘recognize’ each of its homologues (even the distant ones). The extraction process relies on a very ef�cient dynamic programming procedure known as repeated matches (Durbin et al., 1998). This algorithm reports a series of non-overlapping sub-strings each of them having an alignment to the master associated with a score higher than some pre-speci�ed threshold T h. T h is empirically set to be a function of the maser repeat length (L): Th = S ∗ L S has a value between 0 and 1. By default, S = 0.05, but its value can be modi�ed interactively. Two other parameters can also be modi�ed to increase sensitivity and accuracy: the gap opening penalty and the gap extension. Mocca is part of the T-Coffee package. It is written in Perl and ANSI C. It runs on any UNIX or LINUX platform. It is available free of charge along with documentation. Copies can be obtained on request by sending an e-mail to cedric.notredame@gmail.com. The main com2
 
 Mocca and domain hunting
 
@@ -7642,7 +7642,7 @@ Keywords: pair-wise alignment; progressive alignment; local alignment; global al
 
 Introduction
 The simultaneous alignment of three or more nucleotide or amino acid sequences is one of the commonest tasks in bioinformatics. Multiple alignments are an essential pre-requisite to many further analyses of protein families such as homology modeling or phylogenetic reconstruction, or are simply used to illustrate conserved and variable sites within a family. These alignments may be further used to derive pro®les (Gribskov et al., 1987) or hidden Markov models (Bucher et al., 1996; Haussler et al., 1993) that can be used to scour databases for distantly related members of the family. The automatic generation of an accurate multiple alignment is potentially a daunting task. Ideally, one would make use of an in-depth knowledge of the evolutionary and structural relationships within the family, but this information is often
-Abbreviations used: 3D, three-dimensional; SP, sumof-pairs; NBS(s), nucleotide-binding site(s). E-mail address of the corresponding author: cedric.notredame@europe.com
+Abbreviations used: 3D, three-dimensional; SP, sumof-pairs; NBS(s), nucleotide-binding site(s). E-mail address of the corresponding author: cedric.notredame@gmail.com
 0022-2836/00/010205±13 $35.00/0
 
 lacking or dif®cult to use. General empirical models of protein evolution (Benner et al., 1992; Dayhoff, 1978; Henikoff & Henikoff, 1992) are widely used instead, but these can be dif®cult to apply when the sequences are less than 30 % identical (Sander & Schneider, 1991). Further, mathematically sound methods for carrying out alignments, using these models, can be extremely demanding in computer resources for more than a handful of sequences (Carrillo & Lipman, 1988; Wang & Jiang, 1994). In practice, heuristic methods are used for all but the smallest data sets. The most commonly used heuristic methods are based on the progressive-alignment strategy (Feng & Doolittle, 1987; Hogeweg & Hesper, 1984; Taylor, 1988). with ClustalW (Thompson et al., 1994) being the most widely used implementation. The idea is to take an initial, approximate, phylogenetic tree between the sequences and to gradually build up the alignment, following the order in the tree. Although successful in a wide variety of cases, this method suffers from its greediness. Errors made in the ®rst alignments cannot be recti®ed later as the rest of the sequences are added in. T-Coffee is an attempt to minimize that effect, and
@@ -7693,7 +7693,7 @@ Figure 3. Comparison between T-Coffee and Prrp. For each alignment in BaliBase,
 
 T-Coffee: a Method for Sequence Alignment
 
-211 respective publications and installed on our machines. Statistical validation It is critical to establish whether differences observed between two methods are statistically meaningful. We used the same strategy as Gotoh (1996), which involves applying the Wilcoxon signed matched-pair ranked test on the results obtained with two methods on the 141 BaliBase alignments. This non-parametric test allows the association of a P-value with the differences measured on these two series of results. In that case, the P-value is the probability that the observed differences may be due to chance. The lower the P-value, the more signi®cant the result. Implementation T-Coffee is implemented in ANSI C. Its tree-parsing and tree-calculating facilities were taken from the ClustalW package, and it uses a modi®ed version of the Lalign program. T-Coffee is available free of charge on request from the authors and is distributed with documentation and examples (send a request to cedric.notredame@europe.com). Here, the program was run on a LINUX platform with Pentium II processors (330 MHz).
+211 respective publications and installed on our machines. Statistical validation It is critical to establish whether differences observed between two methods are statistically meaningful. We used the same strategy as Gotoh (1996), which involves applying the Wilcoxon signed matched-pair ranked test on the results obtained with two methods on the 141 BaliBase alignments. This non-parametric test allows the association of a P-value with the differences measured on these two series of results. In that case, the P-value is the probability that the observed differences may be due to chance. The lower the P-value, the more signi®cant the result. Implementation T-Coffee is implemented in ANSI C. Its tree-parsing and tree-calculating facilities were taken from the ClustalW package, and it uses a modi®ed version of the Lalign program. T-Coffee is available free of charge on request from the authors and is distributed with documentation and examples (send a request to cedric.notredame@gmail.com). Here, the program was run on a LINUX platform with Pentium II processors (330 MHz).
 
 mostly affect category 4, where four test-cases out of 13 are different between the two releases. Validation is carried out by comparing each calculated multiple alignment with its counterpart in BaliBase. The scoring scheme is the percentage of the trusted columns in the reference that have been correctly aligned. This column-wise comparison has been described as being more sensitive and discriminating (Thompson et al., 1999b) than the alternative pair-wise comparison used by Gotoh (1996), especially in the case of categories 2 and 3 of BaliBase. In the context of this work, the column measure, applied to the trusted regions, is the default that was used to generate our results. For comparison purposes, we also implemented the so-called sum-of-pairs (SP) measure, where a calculated alignment is assessed on proper alignment of all possible pairs of residues in each of the alignment columns. This measure generally leads to a more gradual loss of score in case of misalignment than the above column-count measure. The comparison routine we used was devised following Baliscore, the program made available and used by Thompson et al. (1999b), although some updates were effected to ensure accurate alignment comparison. Comparison with other methods To compare T-Coffee with other methods, we produced multiple alignments of each BaliBase family with other programs. We evaluated three such packages here. They include the methods described as performing best by the authors of BaliBase. Together, they cover a large portion of the existing algorithms for multiple sequence alignments. Prrp (Gotoh, 1996) attempts to simultaneously align all the sequences in an iterative manner. It uses a scoring function very similar to the MSA program (weighted sums of pairs; Lipman et al., 1989). ClustalW (Thompson et al., 1994) is a progressive-alignment method. Dialign2 (Morgenstern, 1999) is a segment-based method that constructs the multiple alignment by assembling a collection of high-scoring segments in a sequence-independent progressive manner. Methods based on multidimensional dynamic programming like MSA (Lipman et al., 1989) or DCA (Stoye, 1998) could not be used in the evaluation as they aborted the construction of alignments in about 10 % of the BaliBase sets. For the alignments that MSA and DCA could construct, the accuracy was comparable to Prrp. We constructed the alignments by extracting the sequences from the BaliBase reference alignments and realigning them with a given program. In each case, the parameters used were the default settings provided by the authors. We made no attempt of tuning, either on T-Coffee and its associated methods, or on the methods used for comparison. The packages used here are those that were available in January 1999 when they were downloaded from the sites indicated by the authors in their
 
@@ -7766,7 +7766,7 @@ INTRODUCTION Over the years, multiple sequence alignment methods have been estab
 these methods is consistently better than the others. For instance, systematic benchmarking experiments carried out with established collections of reference alignments (9) have shown that each available package is better suited than the others to certain types of problems but that none is always the best (10). This situation explains why from one bioinformatics project to the next, the authors often use a different multiple sequence alignment package. Unfortunately it is usually dif�cult to determine which software or algorithm will work best on a given set of sequences and the only way to address this problem is through a tedious trial and error process. This complicated situation makes it critical to ensure that non-specialists have full access to state-of-the-art resources dedicated to multiple sequence alignments. The server we introduce here offers access to the latest version of T-Coffee (11), a recent multiple sequence alignment method. The web interface makes it possible to put some emphasis on important options of this program that are normally buried in the command line syntax. Another advantage of this server is that the people who maintain it also develop the T-Coffee package. This insures that the server always runs the latest version of the package. Several tutorials are available for T-Coffee including one in the book ‘Bioinformatics for dummies’ (12) and another one in preparation for Current Protocols in Bioinformatics. METHODS Multiple sequence alignment assembly T-Coffee is a multiple sequence alignment method. Given a set of pre-selected protein or DNA sequences, T-Coffee computes a multiple sequence alignment of the input sequences. To that effect T-Coffee starts by computing a collection of pair-wise alignments: for each possible pair of sequences in the dataset, the program computes the best global alignment and the 10 best local alignments [using the Sim algorithm from the Lalign package (13)]. This collection of pairwise alignments is named a library in the T-Coffee jargon. In the second step of the procedure T-Coffee assembles a multiple sequence alignment that has the highest possible level of consistency with the alignments within the library. T-Coffee is only a heuristic and the optimality of this process is not guaranteed, although the results are usually satisfactory as judged by comparison with
 Q1
 
-*To whom correspondence should be addressed. Tel: þ33 ???; Fax: þ33 ???; Email: cedric.notredame@europe.com
+*To whom correspondence should be addressed. Tel: þ33 ???; Fax: þ33 ???; Email: cedric.notredame@gmail.com
 
 Nucleic Acids Research, Vol. 31, No. 13 # Oxford University Press 2003; all rights reserved
 
@@ -7831,4 +7831,4 @@ Q5
 
 Please supply publisher’s location
 
-
\ No newline at end of file
+
diff --git a/public_html/Resources/book_list.html b/public_html/Resources/book_list.html
index 85eb2ac..8adfa29 100755
--- a/public_html/Resources/book_list.html
+++ b/public_html/Resources/book_list.html
@@ -96,7 +96,7 @@ <h2><font color="#0000EE">Compiled By Cedric Notredame</font></h2>
 	 
 	  <table>
 	  
-   <p><font size="2">Questions should be sent to <a href="mailto:cedric.notredame@europe.com">C.Notredame</a> </font></center>
+   <p><font size="2">Questions should be sent to <a href="mailto:cedric.notredame@gmail.com">C.Notredame</a> </font></center>
 </center>
  </body>
  </html>
diff --git a/public_html/Resume/resume.html.old b/public_html/Resume/resume.html.old
index e6931dc..15997c3 100755
--- a/public_html/Resume/resume.html.old
+++ b/public_html/Resume/resume.html.old
@@ -24,7 +24,7 @@ Structural Information <BR>CNRS-UMR 1889 <BR>13402 Marseilles Cedex
 </P>
 <P>Tel. : +33 491 165 606 <BR>Fax : +33 491 164 549 
 </P>
-<P STYLE="font-weight: medium">E-mail: cedric.notredame@europe.com
+<P STYLE="font-weight: medium">E-mail: cedric.notredame@gmail.com
 <BR>WWW: http://igs-server.cnrs-mrs.fr/~cnotred/ 
 </P>
 <P><BR><BR>
diff --git a/public_html/Resume/resume.txt b/public_html/Resume/resume.txt
index b471d3b..b28486d 100755
--- a/public_html/Resume/resume.txt
+++ b/public_html/Resume/resume.txt
@@ -6,7 +6,7 @@ CNRS-UMR 1889
 France 
 Tel. : +33 491 165 606 
 Fax : +33 491 164 549 
-E-mail: cedric.notredame@europe.com 
+E-mail: cedric.notredame@gmail.com 
 WWW: http://igs-server.cnrs-mrs.fr/~cnotred/ 
 
 Personal situation 
diff --git a/public_html/Tcoffee.htm b/public_html/Tcoffee.htm
index ebabea2..162ff4a 100755
--- a/public_html/Tcoffee.htm
+++ b/public_html/Tcoffee.htm
@@ -25,7 +25,7 @@
              <a href="http://www.tcoffee.org" style="color: #ffffff;">HOME</a>&nbsp;|&nbsp;
              <a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html" style="color: #ffffff;">references</a>&nbsp;|&nbsp;
              <a href="http://www.igs.cnrs-mrs.fr/Tcoffee/Doc/doc3.html" target="_blank" style="color: #ffffff;">help</a>&nbsp;|&nbsp;
-             <a href="mailto:t_coffee_webmaster@igs.cnrs-mrs.fr,cedric.notredame@europe.com">
+             <a href="mailto:t_coffee_webmaster@igs.cnrs-mrs.fr,cedric.notredame@gmail.com">
                 <img src="http://www.igs.cnrs-mrs.fr/Tcoffee/Images/mail1.gif" alt="e-mail" border="0" /></a>&nbsp;&nbsp;&nbsp;
              <a href="http://www.igs.cnrs-mrs.fr/Tcoffee/tcoffee_cgi/index.cgi?load_cfg_file=1" style="text-decoration: none; color: #000000;">.</a>
            </td>
@@ -258,4 +258,4 @@
 </table><br/>
 
 </body>
-</html>
\ No newline at end of file
+</html>
diff --git a/public_html/Workshops/RNG/list.cvs b/public_html/Workshops/RNG/list.cvs
index 9eaf8a7..84ae69d 100755
--- a/public_html/Workshops/RNG/list.cvs
+++ b/public_html/Workshops/RNG/list.cvs
@@ -23,7 +23,7 @@ duret@biomserv.univ-lyon1.fr ;Laurent Duret;conf
 Pierre.Pontarotti@up.univ-mrs.fr ;Pierre Pontarotti;conférencier
 galtier@crit1.univ-montp2.fr ;Nicolas Galtier;conférencier
 Jean-Michel.Claverie@igs.cnrs-mrs.fr;Jean Michel Claverie;organisateur
-cedric.notredame@europe.com ;Cedric Notredame;organisateur
+cedric.notredame@gmail.com ;Cedric Notredame;organisateur
 Pierre-Edouard.Fournier@medecine.univ-mrs.fr;Pierre-Edourd Fournier;conférencier
 leparco@com.univ-mrs.fr;Yannick LEPARCO ;participant
 serge.champion@pharmacie.univ-mrs.fr;Champion Serge;participant
diff --git a/public_html/Workshops/RNG/x b/public_html/Workshops/RNG/x
index 022af6b..448fcc4 100755
--- a/public_html/Workshops/RNG/x
+++ b/public_html/Workshops/RNG/x
@@ -1 +1 @@
-nicolas.lartillot@lirmm.fr; moszer@pasteur.fr; alex.baumel@univ.u-3mrs.fr;  Virginie.Lopez@up.univ-mrs.fr; darlu@vjf.inserm.fr; edemarsy@ujf-grenoble.fr; letondal@pasteur.fr; regis.mache@ujf-grenoble.fr; Herve.Rique@sanofi-aventis.com; Vincent.Laudet@ens-lyon.fr; mgouy@biomserv.univ-lyon1.fr; celine.brochier@up.univ-mrs.fr; etienne.danchin@afmb.univ-mrs.fr; ewbank@ciml.univ-mrs.fr; gruseas@yahoo.com; cdauga@pasteur.fr; duquenne@biomserv.univ-lyon1.fr; laugraud@biomserv.univ-lyon1.fr; gascuel@lirmm.fr  ; poch@titus.u-strasbg.fr ; perriere@biomserv.univ-lyon1.fr ; duret@biomserv.univ-lyon1.fr ; Pierre.Pontarotti@up.univ-mrs.fr ; galtier@crit1.univ-montp2.fr ; Jean-Michel.Claverie@igs.cnrs-mrs.fr; cedric.notredame@europe.com ; Pierre-Edouard.Fournier@medecine.univ-mrs.fr; leparco@com.univ-mrs.fr; serge.champion@pharmacie.univ-mrs.fr; 
\ No newline at end of file
+nicolas.lartillot@lirmm.fr; moszer@pasteur.fr; alex.baumel@univ.u-3mrs.fr;  Virginie.Lopez@up.univ-mrs.fr; darlu@vjf.inserm.fr; edemarsy@ujf-grenoble.fr; letondal@pasteur.fr; regis.mache@ujf-grenoble.fr; Herve.Rique@sanofi-aventis.com; Vincent.Laudet@ens-lyon.fr; mgouy@biomserv.univ-lyon1.fr; celine.brochier@up.univ-mrs.fr; etienne.danchin@afmb.univ-mrs.fr; ewbank@ciml.univ-mrs.fr; gruseas@yahoo.com; cdauga@pasteur.fr; duquenne@biomserv.univ-lyon1.fr; laugraud@biomserv.univ-lyon1.fr; gascuel@lirmm.fr  ; poch@titus.u-strasbg.fr ; perriere@biomserv.univ-lyon1.fr ; duret@biomserv.univ-lyon1.fr ; Pierre.Pontarotti@up.univ-mrs.fr ; galtier@crit1.univ-montp2.fr ; Jean-Michel.Claverie@igs.cnrs-mrs.fr; cedric.notredame@gmail.com ; Pierre-Edouard.Fournier@medecine.univ-mrs.fr; leparco@com.univ-mrs.fr; serge.champion@pharmacie.univ-mrs.fr; 
\ No newline at end of file
diff --git a/public_html/Workshops/index.html b/public_html/Workshops/index.html
index 260d3e5..ce08b50 100644
--- a/public_html/Workshops/index.html
+++ b/public_html/Workshops/index.html
@@ -56,7 +56,7 @@ <h2><font color="#0000EE">Cedric Notredame</font></h2>
 	</table>
        <BR><BR>
 
-   <p><font size="2">Questions should be sent to <a href="mailto:cedric.notredame@europe.com">C.Notredame</a> </font></center>
+   <p><font size="2">Questions should be sent to <a href="mailto:cedric.notredame@gmail.com">C.Notredame</a> </font></center>
 </center>
  </body>
  </html>
diff --git a/public_html/Workshops/index.html~ b/public_html/Workshops/index.html~
deleted file mode 100644
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-<html>
- <head>
-  <meta http-equiv="content-type" content="text/html;charset=iso-8859-1">
-  <meta name="generator" content="Adobe GoLive 4">
-  <title>Bioinformatics Workshops</title>
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- 
- <center>
-      <table border=10 cellpadding="20" width=40% nosave>
-	<tr>
-	  <td align=center bgcolor="FFCCAA">
-	    <h2>Bioinformatics<BR><BR>Schools and Workshops</h2>
-	    <h2><font color="#0000EE">Cedric Notredame</font></h2>
-	  </td>
-	</tr>
-      </table>
-      <br><br><br>
-      
-      <center>
-	<table BGCOLOR="#FFFFEE" Align="center" cellpadding=30  leftmargin="30" marginwidth="30" width="60%"  border="5"> 
-	  <tr>
-	    <th BGCOLOR="#FFDDAA"><h2>Workshops Archives</h2></th>
-	  </tr>
-
-	  <tr align=center>
-	    <td><font size=+1><A HREF="http://www.gene2farm.eu/index.php/g2fws2013" target="_blank" >Gene2Farm Winter School 2013</a>, UCSC, Piacenza (Italy), November 2013</td>
-	  </tr>
-
-	  <tr align=center>
-	    <td><font size=+1><A HREF="./HPC/HPC_meeting_agenda.pdf" target="_blank">Distributed computation in Biology</a>, CRG, Barcelona (Spain), 20 June 2013</td>
-	  </tr>
-	  <tr align=center>
-	    <td><font size=+1><A HREF="./israel_workshop_2008/index.html">T-Coffee Workshop </a>, Weizmann Institute, Rehovot (Israel), September 2008</td>
-	  </tr>
-	  <tr align=center>
-	    <td><font size=+1>SwissProt T-Coffee Workshop, Geneva (Switzerland), April 2006</td>
-	  </tr>
-	  <tr align=center>
-	    <td><font size=+1><A HREF="./RNG/jrng.html">Réseau National des Génopoles (Phylogeny)<A>, Marseille (France), December 2005</td>
-	  </tr>
-	  
-          <tr align=center>
-	    <td><font size=+1><A HREF="./prosite_workshop/index.html">Prosite Workshop</a>, Marseille (France), July 2002</td>
-	  </tr>
-
-
-          <tr align=center>
-	    <td><font size=+1><A HREF="./tcoffeetutorials/index.html">T-Coffee Workshop</a>, CRG. Barcelona (Spain), 2011</td>
-	  </tr>
-	</table>
-       <BR><BR>
-<tr align=center>
-	    <td><font size=+1><A HREF="./Napoli.EMBO.2012/">Napoli Workshop</a>,EMBO, Napoli, 2012</td>
-	  </tr>
-	</table>
-       <BR><BR>
-
-   <p><font size="2">Questions should be sent to <a href="mailto:cedric.notredame@europe.com">C.Notredame</a> </font></center>
-</center>
- </body>
- </html>
diff --git a/public_html/homepage.html b/public_html/homepage.html
index 1b9f408..e3394ba 100644
--- a/public_html/homepage.html
+++ b/public_html/homepage.html
@@ -360,7 +360,7 @@ <H4>
 				Dr Aiguader, 88                            <br>
 				08003 Barcelona                            <br>
 				Spain                                      <br>
-				Email:  <A href="MAILTO:cedric.notredame@europe.com">cedric.notredame@europe.com</A>    <br>
+				Email:  <A href="MAILTO:cedric.notredame@gmail.com">cedric.notredame@gmail.com</A>    <br>
 				HOME :  <A HREF="http://www.tcoffee.org/homepage.html">http://www.tcoffee.org/homepage.html</A><br>
 			        GROUP:  <a href="https://www.crg.eu/en/programmes-groups/notredame-lab">CRG</A><br>	
 		                Phone   :  +34 933 160 271                <br>
diff --git a/public_html/homepage.html~ b/public_html/homepage.html~
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- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html>
-  <head>
-    <title>Notredame Lab Home Page - Comparative Bioinformatics</title>
-
-<!-- Google tag (gtag.js) -->
-<script async src="https://www.googletagmanager.com/gtag/js?id=G-W0ZCV3Q3DG"></script>
-<script>
-  window.dataLayer = window.dataLayer || [];
-  function gtag(){dataLayer.push(arguments);}
-  gtag('js', new Date());
-
-  gtag('config', 'G-W0ZCV3Q3DG');
-</script>   
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-  <BODY TEXT="#000000" BGCOLOR=white LINK="#0000EE" VLINK="#551A8B" ALINK="#FF0000">
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-	      <table width="100%" cellpadding=15 cellspacing=0 cellborder=0 valign="TOP" border=0>
-		  <tr bgcolor="#FFEBCD" >
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-		  
-		  <tr>
-		    <td colspan=5 bgcolor="#FFEBCD">
-		      <center><table><tr><td align="center"><b> <FONT size="7" color="#8B4513">Notredame's Lab<br>Comparative Bioinformatics</font></b></td></tr></table></center>
-		    </td>
-		  </tr>
-		  
-		  <tr>
-		    <td colspan=5 bgcolor="#FFEBCD"><br></td>
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-		      <HR>
-		      <center>
-			<table width="100%" cellpadding=15 cellspacing=0 cellborder=0 valign=top>
-			    <tr align=center>
-			      <td width="15%" onMouseOver="style.backgroundColor='white';"onmouseout="style.backgroundColor='#FFE4C4'"><b><a href="https://www.crg.eu/en/programmes-groups/notredame-lab"><font color="#8B4513">GROUP</font></a></b></td>
-			      <td width="15%" onMouseOver="style.backgroundColor='white';"onmouseout="style.backgroundColor='#FFE4C4'"><b><a href="http://tcoffee.crg.cat"><font color="#8B4513">SERVERS</font></a></b></td>
-			      <td width="15%" onMouseOver="style.backgroundColor='white';"onmouseout="style.backgroundColor='#FFE4C4'"><b><a href="./Projects/tcoffee/index.html"><font color="#8B4513">T-COFFEE</font></a></b></td>
-			      <td width="15%" onMouseOver="style.backgroundColor='white';"onmouseout="style.backgroundColor='#FFE4C4'"><b><a href="#RESEARCH"><font color="#8B4513">RESEARCH</font></a></b></td>
-			      <td width="15%" onMouseOver="style.backgroundColor='white';"onmouseout="style.backgroundColor='#FFE4C4'"><b><a href="#TEACHING"><font color="#8B4513">TEACHING</font></a></b></td>
-			      <td width="15%" onMouseOver="style.backgroundColor='white';"onmouseout="style.backgroundColor='#FFE4C4'"><b><a href="#CONTACT"><font color="#8B4513">CONTACT</font></a></b></td>
-			      <td width="15%" onMouseOver="style.backgroundColor='white';"onmouseout="style.backgroundColor='#FFE4C4'"><b><a href="./Packages/"><font color="#8B4513">DOWNLOADS</font></a></b></td>
-			      <td width="15%" onMouseOver="style.backgroundColor='white';"onmouseout="style.backgroundColor='#FFE4C4'"><b><a href="./Jobs/index.html"><font color="#8B4513">JOBS</font></a></b></td>
-			      
-			    </tr>
-			    
-			</table>
-		      </center>
-		      <HR>
-		    </td>
-		  </tr>
-		  
-		  <tr>
-		    <td colspan=5 bgcolor="#FFEBCD"><br></td>
-		  </tr>
-		  
-		  <tr>
-		    <td rowspan=1 bgcolor="#FFEBCD"><br></td>
-		    <td colspan=3 rowspan=1 bgcolor="white" valign="top">
-		      <center><h2><FONT color="#8B4513">WELCOME!</FONT></h2></center>
-		      <table bgcolor="white">
-			  <tr>
-			    <td>
-			      <p align="justify">
-			     Welcome to the <A target="_blank" HREF="https://www.crg.eu/en/programmes-groups/notredame-lab">Comparative Bionformatics Group Homepage</A>(aka Notredame's lab) a research group of the <A HREF="http://www.crg.es" target="_blank">Center for Genomic Regulation</A> in Barcelona. The main focus of our group is the development of novel algorithms for the comparison of multiple biological sequences. Multiple comparisons have the advantage of precisely revealing evolutionary traces, thus allowing the identification of functional constraints imposed on the evolution of biological entities. Most comparisons are currently carried out on the basis of sequence similarity. Our goal is to extend this scope by allowing comparisons based on any relevant biological signal such as sequence homology, structural similarity, genomic structure, functional similarity and more generally any signal that may be identified within biological sequences. Using such heterogeneous signals serves two complementary purposes: (i) producing better models that take advantage of the signal evolutionary resilience, (ii) improving our understanding of the evolutionary processes that lead to the diversification of biological functions. All the applications related to our work are provided to the community through an international network of web servers that can be accessed from <a href="http://tcoffee.crg.cat" target="_blank">server.tcoffee.org</a>.</P> 
-			    </td>
-			  </tr>
-		      </table>
-		      
-		    </td>
-		    
-		    <td colspan=1 rowspan=1 bgcolor="#FFEBCD"><br></td>
-		  </tr>
-		  
-		  <tr>
-		    <td colspan=5 bgcolor="#FFEBCD"><br></td>
-		  </tr>
-
-		  <tr>
-		    <td colspan=1 rowspan=1 bgcolor="#FFEBCD"><br></td>
-		    <td colspan=3 rowspan=1 bgcolor="white" align="center">
-		      <center><h2><FONT color="#8B4513"><a name="RESEARCH">RESEARCH PROJECTS</a></font></h2></center>
-		      <table bgcolor="white">
-			  <tr>
-			    <td>
-			      <table>
-				  <tr><td colspan=4><BR></td></tr>
-				  <tr>
-				    <td><b>T-Coffee</b></td>
-				    <td>A Multiple Sequence Alignment Package</td>
-				    <td><A HREF="Projects/tcoffee/index.html"><b>homepage</b></A></td>
-				    <td><A HREF="Projects/tcoffee/presentations/tcoffee.ppt"><b>ppt</b></A></td>
-				    <td><A HREF="http://www.tcoffee.org"><b>server</b></A></td>
-
-			    </tr>
-			    <tr><td colspan=4><hr></td></tr>
-				  <tr>
-				    <td><b>TCS</b></td>
-				    <td>Evaluation and filtering of multiple Sequence Alignments</td>
-				    <td><A HREF="Projects/tcs/index.html"><b>homepage</b></A></td>
-				    <td><b>ppt</b></td>
-				    <td><A HREF="http://tcoffee.crg.cat/apps/tcoffee/do:core"><b>server</b></A></td>
-				
-			    </tr>
-			    <tr><td colspan=4><hr></td></tr>
-				  <tr>
-				    <td><b>M-Coffee</b></td>
-				    <td>Combination of Multiple Sequence Alignment Packages</td>
-				    <td><A HREF="./Projects/mcoffee/index.html"><b>homepage</b></A></td>
-				    <td><A HREF="./Projects/mcoffee/presentations/mcoffee.ppt"><b>ppt</b></A></td>
-				    <td><A HREF="http://www.tcoffee.org"><b>server</b></A></td>
-				
-			    </tr>
-				  <tr><td colspan=4><hr></td></tr>
-				  <tr>
-				    <td><b>3D-Coffee/Expresso</b></td>
-				    <td>Combination of Sequences and Structures</td>
-				    <td><A HREF="./Projects/expresso/index.html"><b>homepage</b></A></td>
-				    <td><A HREF="./Projects/expresso/presentations/3dcoffee.ppt"><b>ppt</b></A></td>
-				    <td><A HREF="http://www.tcoffee.org"><b>server</b></A></td>
-				    
-				  </tr>
-				  <tr><td colspan=4><hr></td></tr>
-				  <tr>
-				    <td><b>R-Coffee</b></td>
-				    <td>RNA Multiple Sequence Alignment</td>
-				    <td><A HREF="Projects/rcoffee/index.html"><b>homepage</b></A></td>
-				    <td><A HREF="Projects/rcoffee/presentations/rcoffee.ppt"><b>ppt</b></A></td>
-				    <td><A HREF="http://www.tcoffee.org"><b>server</b></A></td>
-
-				  </tr>
- 
-				  <tr><td colspan=4><hr></td></tr>
-				  <tr>
-				    <td><b>Sara-Coffee</b></td>
-				    <td>RNA Multiple Sequence Alignment Using Structural Information</td>
-				    <td><A HREF="Projects/saracoffee/index.html"><b>homepage</b></A></td>
-			          </tr>
-			    
-			          <tr><td colspan=4><hr></td></tr>
-				  <tr>
-				    <td><b>T-RMSD</b></td>
-				    <td>T-RMSD   Structure based clustering</td>
-				    <td><A HREF="Projects/trmsd/index.html"><b>homepage</b></A></td>
-				    <td><A HREF="Projects/trmsd/presentations/trmsd.ppt"><b>ppt</b></A></td>
-				    <td>&nbsp;</td>
-				  </tr>
-
-
-				  <tr><td colspan=4><hr></td></tr>
-				  <tr>
-				    <td><b>MOCCA</b></td>
-				    <td>Repeat Discovery with T-Coffee</td>
-				    <td><A HREF="Projects/mocca/index.html"><b>homepage</b></A></td>
-				    <td><BR></td>
-				  </tr>
-				  <tr><td colspan=4><hr></td></tr>
-				  <tr>
-				    <td><b>SAGA and Coffee</b></td>
-				    <td>Multiple Protein Alignment by Genetic Algorithm</td>
-				    <td><A HREF="Projects/saga/index.html"><b>homepage</b></A></td>
-				    <td><A HREF="Projects/saga/presentations/saga.ppt"><b>ppt</b></A></td>
-				    <td><BR></td>
-
-				  </tr>
-				  <tr><td colspan=4><hr></td></tr>
-				  <tr>
-				    <td><b>(P)RAGA</b></td>
-				    <td>RNA Alignment by Genetic Algorithm</td>
-				    <td><A HREF="Projects/raga/index.html"><b>homepage</b></A></td>
-				    <td><A HREF="Projects/raga/presentations/raga.ppt"><b>ppt</b></A></td>
-				    <td><BR></td>
-				  </tr>
-
-				  <tr><td colspan=4><hr></td></tr>
-				  <tr>
-				    <td><b>Blast-R</b></td>
-				    <td>Fast and accurate database searches for non-coding RNAs</td>
-				    <td><A HREF="Projects/blastr/index.html"><b>homepage</b></A></td>
-				    <td>&nbsp;</td>
-				    <td><BR></td>
-				  </tr>
-				  
-				  <tr><td colspan=4><hr></td></tr>
-				  <tr>
-				    <td><b>Strike</b></td>
-				    <td>A sequence alignment scoring tool</td>
-				    <td><A HREF="Projects/strike/index.html"><b>homepage</b></A></td>
-				    <td>&nbsp;</td>
-			      <td><BR></td>
-				  </tr>
-				  
-				  <tr><td colspan=4><hr></td></tr>
-				  <tr>
-				    <td><b>Pro-Coffee</b></td>
-				    <td>Aligns homologous promoter regions</td>
-				    <td><A HREF="Projects/procoffee/index.html"><b>homepage</b></A></td>
-				    <td>&nbsp;</td>
-			      <td><BR></td>
-				  </tr>
-				 
-                                  <tr><td colspan=4><hr></td></tr>
-                                  <tr>
-                                    <td><b>Nextflow</b></td>
-                                    <td>Data-driven computational toolkit for highly scalable pipelines</td>
-                                    <td><A HREF="http://www.nextflow.io" target='_blank'><b>homepage</b></A></td>
-                                    <td>&nbsp;</td>
-                              <td><BR></td>
-                                  </tr>
- 
-			      </table>
-			    </td>
-			  </tr>
-		      </table>
-		    <td colspan=1 rowspan=1 bgcolor="#FFEBCD"><br></td>
-		  </tr>
-		  
-		  <tr>
-		    <td colspan=5 rowspan=1 bgcolor="#FFEBCD"><br></td>
-		  </tr>
-		  
-		  <tr>
-		    <td colspan=1 rowspan=1 bgcolor="#FFEBCD"><br></td>
-		    <td colspan=1 rowspan=1 bgcolor="white" align="center">
-		      <center><h2><FONT color="#8B4513"><a name="TEACHING">TEACHING</a></font></h2></center>
-		      <table bgcolor="white">
-			  <tr>
-			    <td align="center">
-			      <table>
-				  <tr>
-				    <td><b>Courses and Lectures</b></td>
-				    <td><b>[<A href="Courses/Exercises/index.html">web</a>]</b></td>
-				  </tr>
-				  <tr>
-				    <td><b>Workshops</b></td>
-				    <td><b>[<a href="Workshops/index.html">web</A>]</b></td>
-				  </tr>
-				  
-			      </table>
-			    </td>
-			  </tr>
-		      </table>
-		    </td>
-		    <td colspan=1 bgcolor="#FFEBCD"><br></td>
-		    <td colspan=1 rowspan=1 bgcolor="white">
-		      <center><h2><FONT color="#8B4513"><a name="PUBLICATIONS">PUBLICATIONS</a></font></h2></center>
-		      <table bgcolor="white">
-			  <tr>
-			    <td>
- The Medline list of the lab's publications is available on <b>[<a href="http://www.ncbi.nlm.nih.gov/pubmed/20887892,20868492,20838655,20614016,20605929,20471393,20205190,20080951,19648142,19008347,18689823,18483080,18428722,18420654,17973996,17784778,17526519,17032685,16873492,16845081,16845080,16556910,15215460,15215345,15201059,14649299,12855461,12824354,11966409,11301309,10964570,11125048,9682054,9632828,9358168,8628686,">Medline</a>]</b>.
-
-			    </td>
-			  </tr>
-			  <tr>
-			    <td>
-			      Some of our papers are available as <b>[<a href="Publications/Pdf/">PDF preprints</a>]</b>
-			    </td>
-			  </tr>
-			  <tr>
-			    <td>
-			      My PhD
-			      <b>[<A HREF="Publications/Ps_pdf/phd_intro.ps.gz">ps</A>]</b>
-			      <b>[<A HREF="Publications/Ps_pdf/phd_intro.pdf">pdf</A>]</b>
-			    </td>
-			  </tr>
-		      </table>
-		    </td>
-		    <td rowspan=1 bgcolor="#FFEBCD"><br></td>
-		  </tr>
-		  
-		  <tr>
-		    <td colspan=5 rowspan=1 bgcolor="#FFEBCD"><br></td>
-		  </tr>
-		  
-		  <tr>
-		    <td colspan=1 rowspan=1 bgcolor="#FFEBCD"><br></td>
-		    <td colspan=1 rowspan=1 bgcolor="white" valign="TOP">
-		      <center><h2><FONT color="#8B4513"><a name="LINKS">LINKS</a></font></h2></center>
-		      <table bgcolor="white">
-			  <tr>
-			    <td>
-			      <table>
-				  <tr>
-				    <td><b><A HREF="http://tcoffee.crg.cat" target='_blank'>T-Coffee</a></b></td>
-				    <td><b>Multiple Sequence Alignments Online</b></td>
-				  </tr>
-				  <tr>
-				    <td><b><A HREF="https://github.com/cbcrg/tcoffee" target='_blank'>Github</a></b></td>
-				    <td><b>Repository where you can download T-Coffee source code</b></td>
-				  </tr>
-				  <tr>
-				    <td><b><A HREF="Resources/aligner_list.html" >Alignment Links</a></b></td>
-				    <td><b>Structure and Sequence Alignment Packages</b></td>
-				  </tr>
-				  <tr>
-				    <td><b><A HREF="Resources/book_list.html">Books</b></td>
-				    <td><b>My Favorite Scientific Books</b></td>
-				  </tr>
-				  <tr>
-				    <td><b><a target='_blank' HREF="http://www.dummies.com/WileyCDA/DummiesTitle/productCd-0470089857,page-1.html">Dummies</a></b></td>
-				    <td><b>Bioinformatics For Dummies Links</b></td>
-				  </tr>
-				  <tr>
-				    <td><b><a target='_blank' HREF="http://evolution.genetics.washington.edu/phylip.html">Trees</a> </b></td>
-				    <td><b>THE site for phylogeny</b></td>
-				  </tr>
-				 
-				   <tr>
-				    <td><b><a target='_blank' href="http://ch.embnet.org">EMBnet</b></td>
-				    <td><b>Online Tools at the Swiss EMBnet</b></td>
-				  </tr>
-				   <tr>
-				    <td><b><a target='_blank' href="http://www.expasy.org">ExPasy</a></b></td>
-				    <td><b>SwissProt Home</b></td>
-				  </tr>
-				</table>
-			    </td>
-			  </tr>
-		      </table>
-		    </td>
-		    <td colspan=1 rowspan=1 bgcolor="#FFEBCD"><br></td>
-		    <td colspan=1 rowspan=1 bgcolor="white">
-		      <center><h2><FONT color="#8B4513"><a name="CONTACT">CONTACT</a></font></h2></center>
-		      <table bgcolor="white">
-			  <tr>
-			    <td>
-			      <H4>
-				<br>
-				<code>
-				  <br><br>
-				*******************************************<br>
-				Dr. Cedric Notredame, PhD.                 <br>       
-				Group Leader                               <br>
-				Comparative Bioinformatics Group           <br>
-				Bioinformatics and Genomics Programme      <br>
-				Center for Genomic Regulation (CRG)        <br>
-				Dr Aiguader, 88                            <br>
-				08003 Barcelona                            <br>
-				Spain                                      <br>
-				Email:  <A href="MAILTO:cedric.notredame@europe.com">cedric.notredame@europe.com</A>    <br>
-				HOME :  <A HREF="http://www.tcoffee.org/homepage.html">http://www.tcoffee.org/homepage.html</A><br>
-			        GROUP:  <a href="https://www.crg.eu/en/programmes-groups/notredame-lab">CRG</A><br>	
-		                Phone   :  +34 933 160 271                <br>
-				*******************************************       <br>
-			      </code>
-			      </H4>
-			    </td>
-			  </tr>
-		      </table>
-		    </td>
-		    <td rowspan=1 bgcolor="#FFEBCD"><br></td>
-		  </tr>
-		  <tr>
-		    <td colspan=5 bgcolor="#FFEBCD"><br></td>
-		  </tr>
-		  
-
-		  <tr>
-		    <td colspan=5 bgcolor="#FFE4C4">
-		      <HR>
-		      <center>
-			<table width="100%" cellpadding=15 cellspacing=0 cellborder=0 valign=top>
-			    <tr align=center>
-			      <td width="15%" onMouseOver="style.backgroundColor='white';"onmouseout="style.backgroundColor='#FFE4C4'"><b><a href="https://www.crg.eu/en/programmes-groups/notredame-lab"><font color="#8B4513">GROUP</font></a></b></td>
-			      <td width="15%" onMouseOver="style.backgroundColor='white';"onmouseout="style.backgroundColor='#FFE4C4'"><b><a href="http://tcoffee.crg.cat"><font color="#8B4513">SERVERS</font></a></b></td>
-			      <td width="15%" onMouseOver="style.backgroundColor='white';"onmouseout="style.backgroundColor='#FFE4C4'"><b><a href="./Projects/tcoffee/index.html"><font color="#8B4513">T-COFFEE</font></a></b></td>
-			      <td width="15%" onMouseOver="style.backgroundColor='white';"onmouseout="style.backgroundColor='#FFE4C4'"><b><a href="#RESEARCH"><font color="#8B4513">RESEARCH</font></a></b></td>
-			      <td width="15%" onMouseOver="style.backgroundColor='white';"onmouseout="style.backgroundColor='#FFE4C4'"><b><a href="#TEACHING"><font color="#8B4513">TEACHING</font></a></b></td>
-			      <td width="15%" onMouseOver="style.backgroundColor='white';"onmouseout="style.backgroundColor='#FFE4C4'"><b><a href="#CONTACT"><font color="#8B4513">CONTACT</font></a></b></td>
-			      <td width="15%" onMouseOver="style.backgroundColor='white';"onmouseout="style.backgroundColor='#FFE4C4'"><b><a href="./Packages/"><font color="#8B4513">DOWNLOADS</font></a></b></td>			      
-			      <td width="15%" onMouseOver="style.backgroundColor='white';"onmouseout="style.backgroundColor='#FFE4C4'"><b><a href="./Jobs/index.html"><font color="#8B4513">JOBS</font></a></b></td>
-			    </tr>
-			    
-			</table>
-		      </center>
-		      <HR>
-		    </td>
-		  </tr>
-	    </td>
-	  </tr>
-      </table>
-    </td>
-    </tr>
-    </table>
-    </center>
-  </font>
-  </body>
-</html>
diff --git a/public_html/index_cnrs.html b/public_html/index_cnrs.html
index ff7bc3b..54e9403 100755
--- a/public_html/index_cnrs.html
+++ b/public_html/index_cnrs.html
@@ -25,7 +25,7 @@
              <a href="http://www.tcoffee.org" style="color: #ffffff;">HOME</a>&nbsp;|&nbsp;
              <a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html" style="color: #ffffff;">references</a>&nbsp;|&nbsp;
              <a href="http://www.igs.cnrs-mrs.fr/Tcoffee/Doc/doc3.html" target="_blank" style="color: #ffffff;">help</a>&nbsp;|&nbsp;
-             <a href="mailto:t_coffee_webmaster@igs.cnrs-mrs.fr,cedric.notredame@europe.com">
+             <a href="mailto:t_coffee_webmaster@igs.cnrs-mrs.fr,cedric.notredame@gmail.com">
                 <img src="http://www.igs.cnrs-mrs.fr/Tcoffee/Images/mail1.gif" alt="e-mail" border="0" /></a>&nbsp;&nbsp;&nbsp;
              <a href="http://www.igs.cnrs-mrs.fr/Tcoffee/tcoffee_cgi/index.cgi?load_cfg_file=1" style="text-decoration: none; color: #000000;">.</a>
            </td>
@@ -268,4 +268,4 @@
       <br/>
 
 </body>
-</html>
\ No newline at end of file
+</html>
diff --git a/public_html/index_sib.html b/public_html/index_sib.html
index 54e855f..b382c8c 100755
--- a/public_html/index_sib.html
+++ b/public_html/index_sib.html
@@ -41,7 +41,7 @@
              <a href="http://www.tcoffee.org" style="color: #ffffff;">HOME</a>&nbsp;|&nbsp;
              <a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html" style="color: #ffffff;">references</a>&nbsp;|&nbsp;
              <a href="http://tcoffee.vital-it.ch/Doc/doc3.html" target="_blank" style="color: #ffffff;">help</a>&nbsp;|&nbsp;
-             <a href="mailto:cedric.notredame@europe.com">
+             <a href="mailto:cedric.notredame@gmail.com">
                 <img src="./Images/mail1.gif" alt="e-mail" border="0" /></a>&nbsp;&nbsp;&nbsp;
              <a href="http://tcoffee.vital-it.ch/cgi-bin/Tcoffee/tcoffee_cgi/index.cgi?load_cfg_file=1" style="text-decoration: none; color: #000000;">.</a>
            </td>
@@ -277,4 +277,4 @@
     </td>
   </tr>
 </table><br/>
-</body></html>
\ No newline at end of file
+</body></html>
diff --git a/public_html/index_sib.ref b/public_html/index_sib.ref
index 564141f..bf81ad9 100755
--- a/public_html/index_sib.ref
+++ b/public_html/index_sib.ref
@@ -41,7 +41,7 @@
              <a href="http://www.tcoffee.org" style="color: #ffffff;">HOME</a>&nbsp;|&nbsp;
              <a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html" style="color: #ffffff;">references</a>&nbsp;|&nbsp;
              <a href="http://tcoffee.vital-it.ch/Doc/doc3.html" target="_blank" style="color: #ffffff;">help</a>&nbsp;|&nbsp;
-             <a href="mailto:cedric.notredame@europe.com">
+             <a href="mailto:cedric.notredame@gmail.com">
                 <img src="http://tcoffee.vital-it.ch/Images/mail1.gif" alt="e-mail" border="0" /></a>&nbsp;&nbsp;&nbsp;
              <a href="http://tcoffee.vital-it.ch/cgi-bin/Tcoffee/tcoffee_cgi/index.cgi?load_cfg_file=1" style="text-decoration: none; color: #000000;">.</a>
            </td>
@@ -277,4 +277,4 @@
     </td>
   </tr>
 </table><br/>
-</body></html>
\ No newline at end of file
+</body></html>
diff --git a/public_html/saltt/index.html b/public_html/saltt/index.html
index 773c3dd..f1b6f8b 100755
--- a/public_html/saltt/index.html
+++ b/public_html/saltt/index.html
@@ -205,7 +205,7 @@ <H1>PAVIE PROJECT</H1>
         <LI><H3><FONT COLOR="#8B4513">Tutorial and examples</FONT></H3></LI>
         <LI><H3><FONT COLOR="#8B4513">Related Links</FONT></H3></LI>
         <LI><H3><FONT COLOR="#8B4513">Contact</FONT></H3></LI>
-        Email   :  <A MAILTO="cedric.notredame@europe.com">cedric.notredame@europe.com</A>    <br>
+        Email   :  <A MAILTO="cedric.notredame@gmail.com">cedric.notredame@gmail.com</A>    <br>
  
       </UL>
        
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-   <META NAME="Author" CONTENT="cedric Notredame">
-   <META NAME="Keywords" CONTENT="Sociological data analysis">
-   <TITLE>Pavie Matrix Project Home page</TITLE>
-</HEAD>
-<BODY TEXT="#000000" BGCOLOR="#FFEBCD" LINK="#0000EE" VLINK="#551A8B" ALINK="#FF0000">
-
-<HR WIDTH="100%"></H1>
-
-<H1>PAVIE PROJECT</H1>
-<HR WIDTH="100%">
-
-<P>This page centralizes all the code information relative to the PAVIE/Bioinformatics project, a collaboration between the PAVIE  (Jacques-Antoine Gauthier and Eric Widmer) and the Swiss Institute of Bioinformatics (Philipp Bucher, Cedric Notredame)</P>
-
-<UL>
-<LI><H2><FONT COLOR="#8B4513">Project #1: Matrix Training</FONT></H2></LI>
-    <UL>
-        <P>
-      <LI><H3><FONT COLOR="#8B4513">Accessing and running the algorithms</FONT></H3></LI>
-          <P><UL>
-            <LI>Install the latest <a href="../Packages/T-COFFEE_distribution.tar.gz">T-Coffee distribution </a> in which saltt is incorporated</LI>
-            <LI>Use the <a href="./saltt_doc.doc">documentation</a> along with the following sample <a href=pavie_full.seq>sequences</a></LI>
-          </UL></P> 
-
-        <LI><H3><FONT COLOR="#8B4513">Training Matrices</FONT></H3></LI>
-            <UL>
-                <LI>Your sequences must be in FASTA format:<PRE>
-            seq_reformat -in |<i>your sequences</i>| -action +pavie_seq2pavie_mat [_IDXX_TWEXX[THRid]_[CHANNELn]</PRE></LI>
-                <LI>The program runs iteratively. It starts with the ID matrix and updates its matrix until convergeance is reached.</LI>
-                <LI><b>Weight: _TWEXX_</b></LI>
-                <UL>
-                   <p>Various mode of identity measure are implemented (Trainning WEighting)</p>
-                    <LI>_TWE00_: No weighting</LI>
-                    <LI>_TWE01_: Default, n_id_pairs/n_match</LI>
-                    <LI>_TWE02_: n_id_pairs/aln_length</LI>
-                    <LI>_TWE03_: n_id_pairs/MIN(length seq1, length seq2)<b>Default</b></LI>
-                    <LI>_TWE04_: n_id_pairs/MAX(length seq1, length seq2)<b>Default</b></LI>
-                    <LI>_TWE05_: score as measured with the matrix<b></b></LI> 
-                    <LI>simweight: <b>NOT SUPPORTED ANYMORE</b></LI>
-                </UL>
-                <LI><b>_THRid_</b></LI>
-                <UL>
-                    <LI>_THRid_: id is a threshold that filters alignments. For instance, with THR50, the program will only extract the counts from alignments with more than 50% ID or SIM (depending on the weighmode). The purpose of this filter is to discard bad alignments that should not contribute at all to the final matrix</LI>
-               </UL>
-               <LI><b>_SAMPLEn_</b></LI>
-               <UL>
-                    <LI>_SAMPLEn_: n is the number of random pairs sampled (without removal) at each training round. The pairs change at each round</LI>
-                    <LI>_SAMPLE100_: will randomly select 100 pairs (different at each round)</LI>
-                    <LI>_SAMPLE0_: will select all the pairs (Default)</LI> 
-               </UL>
-               
-               <LI><b>Identity Measure: _IDX_</b></LI>
-               <UL>
-                    <p>Various mode of identity measure are implemented</p>
-                    <LI>_ID01_: Default, n_id_pairs/n_match</LI>
-                    <LI>_ID02_: n_id_pairs/aln_length</LI>
-                    <LI>_ID03_: n_id_pairs/MIN(length seq1, length seq2)</LI>
-                    <LI>_ID04_: n_id_pairs/MAX(length seq1, length seq2)</LI>
-                    <LI>_ID05_: score as measured with the matrix<b>[Not implemented]</b></LI>
-               </UL>
-               
-               <LI><b>_CHANNELn_: multiple channel strings</b></LI>
-               <UL>
-                    <LI>_CHANNELn_: n is the number channels in the FASTA sequences. </LI>
-                    <LI>_CHANNELn_: By default, n is set to 1</LI>
-                    <LI><b>Principle for multiple channel matrix training</b>
-	                <UL>
-	                   <LI>One can use as many channels as required.</LI>
-	                   <LI>Alphabets are totally independant (i.e. each channel can use the same alphabet)</LI>
-	                   <LI>All the channels are simultaneouslz compared and one matrix per channel is estimated</LI>
-	                   <LI>Using pavie_seq2pavie_aln, it is possible to use multiple channle matrices to align multiple channel strings</LI>
-	               </UL>
-	            <LI><b>Rules for multiple channel strings</b></LI>
-                    <UL>
-                        <LI>All the channels are in the same FASTA file</LI>
-                        <LI>All the string of Channel X are grouped</LI>
-                        <LI>All the channels must contains EXACTLY the same number of strings</LI>
-                        <LI>String N of channel X CORRESPONDS to string N of channel Y</LI>
-                        <LI>String N of channel X Must have the same lenght as string N of channel Y</LI>
-                   </UL>
-                   <LI><b>Adding the age in the multichanneling</b></LI>
-                       <UL>
-                           <LI>The age can be used as a channel</LI>
-                           <LI>36 symbols (A-Z0-9) are available 
-                   </UL>
-                   <LI><b>Example of Multi-Channel FASTA file (Names are arbitrary): File: myseq.fasta</b>
-                   <PRE>
-                            >string1.channel1
-                             abcdef
-                            >string2.channel1
-                             ab
-                            >string3.channel1
-                             abc
-                            >string1.channel2
-                             abzeff
-                            >string2.channel2
-                             ef
-                            >string3.channel2
-                             fxx
-                         </PRE>
-                        
-               </UL>
-               <LI><b>Examples of command Lines</b></LI>
-               <UL>
-                    <LI>Defaults: without any extra parameter THR0_SAMPLE0 is assumed. The weight mode must be specified</LI>
-                    <LI><b>EXAMPLE:</b> seq_reformat -in myseq.fasta -action +pavie_seq2pavie_mat _SAMPLE10_TWE00_CHANNEL2_</LI>
-                    <LI><b>EXAMPLE:</b> seq_reformat -in myseq.fasta -action +pavie_seq2pavie_mat _SAMPLE10_TWE00_</LI>
-                    <LI><b>EXAMPLE:</b> seq_reformat -in myseq.fasta -action +pavie_seq2pavie_mat _TWE01_THR40_SAMPLE20_</LI>
-                    <LI><b>EXAMPLE:</b> seq_reformat -in myseq.fasta -action +pavie_seq2pavie_mat _THR40_SAMPLE20_TWE02_</LI>
-              </UL>  
-              <LI>The trainning procedure outputs two series of file:</LI>
-              <UL>
-                  <LI>Matrix file     : <i>pavie_matrix.ch_#.cy_#.pavie_mat</i> that contain a matrix describing the specified chanel</LI>
-                  <LI>Matrix list file: <i>pavie_matrix.cy_#.mat_list</i> that contain a list of matrix files</LI>
-	          <LI>Matrix list file: can be used to compute alignments (next section)</LI>
-              </UL>
-      </UL>
-      <LI><H3><FONT COLOR="#8B4513">Using the age as a channel</FONT></H3></LI>
-      <UL>
-          <P>
-	  It is possible to use the age as a channel. This simply requires generating two extra channels that will be used to encode the age, along with the associated substitution matrices <P>
-	  <UL>
-	     <LI><PRE><b>EXAMPLE:</b>seq_reformat -in myseq.fasta -output pavie_age_channel -out xyz</PRE></LI>
-      	     <LI>xyz_pavie_age_matrix.mat_list is a mat list that must be concatenated to the other mat list (cf multi channeling)</LI>
-             <LI>xyz_pavie_age_matrix.mat_list is a mat list that must be concatenated to the other sequence file (cf multi-channeling)</LI>
-             <LI>xyz_age_channel.fasta contains the sequences recoded (decades: channel1, years: channel2). These sequences must be concatenated to the other channels, as indicated in the channel section</LI>
-             <LI><b>Note:</b> In the age_sequences, A=0...J=9</LI>
-             <LI><b>Note:</b> It is possible to set the year corresponding to the first symbol of a sequence in the header:
-                              <PRE>>name _FIRSTYEARXX_</PRE>
-	                      where XX will be used as the offset of the first year</PRE>
-	     <LI><b>Note:</b> Gaps are ignored<\LI> 
-	 </UL></P>
-	 
-      </UL>
-      <LI><H3><FONT COLOR="#8B4513">Validation of The Training Procedure</FONT></H3></LI>
-      <UL>
-          <P>
-	  Validation is made by replacing a symbol (a for instance) with two other arbitrarily chosen symbols 
-          (c and d) that are otherwise absent from the sequences. The substitution is made across the entire sequence set</P>
-	  <P>
-	  The new dataset should then be used to train a matrix. If the trainning procedure is adequate, the matrix should have the following properties:</P>
-	  <p><UL>
-	     <LI>cost[c][d]=cost[d][c] ~ 0</LI>
-	     <LI>cost[c][x]~cost[d][x]</LI>
-	     </UL></P>
-	  <P>The random sequences can be generated as folows:</P>
-	  <PRE><b>EXAMPLE:</b> seq_reformat -in myseq.fasta -action +pavie_seq2random_seq axw > outseq</PRE>
-	  <P> in this case, axw indicates that a will be replaced with x OR w</P>
-	</UL>
-    <LI><H3><FONT COLOR="#8B4513">Clustering Sequences: Distance Matrix Computation</FONT></H3></LI>
-            <UL>
-               <LI>Given a trained matrix (previous bullet), it is possible to compute all the alignments 
-	and the associated distance matrix betwween all the sequences (SA format). It is also possible to 
-	specify the measure that will be used to output the distances.</LI>
-               <LI>Parameters
-               <UL>
-                  <LI>_MATDIST_: a distance   matrix, where the distance measure mode can be specified with _IDX_</LI>
-                  <LI>_MATSIM_ : a similarity matrix, where the distance measure mode can be specified with _IDX_</LI>
-                  <LI>_IDXX_: the default is _ID01_</LI>
-               </UL></LI>
-               <LI>Example
-               <PRE><b>EXAMPLE:</b> seq_reformat -in myseq.fasta -action +pavie_seq2pavie_aln pavie_matrix.cycle_1.mat_list _MATDIST_ID01_</PRE></LI>
-               <LI>matrix_list</LI> 
-	           <UL>
-	           <LI>file containing the name of valid matrix files.</LI> 
-                   <LI>The number of matrices defines the number of channel in the sequences (cf CHANNEL option).</LI>
-                   <LI>A matrix_list file is output automatically when trainning matrices.</LI>
-                   </UL>
-                </LI>
-            </UL>  
-	  
-
-      <LI><H3><FONT COLOR="#8B4513">Computing Alignments</FONT></H3></LI>
-            <UL>
-                <LI>Given a trained matrix (previous bullet), it is possible to compute all the alignments:
-                <PRE>EXAMPLE: seq_reformat -in myseq -action +pavie_seq2pavie_aln pavie_matrix_.cy_0.mat_list |</PRE></LI>
-                <LI>matrix_list
-	           <UL>
-	              <LI>file containing the name of valid matrix files.</LI> 
-                      <LI>The number of matrices defines the number of channel in the sequences (cf CHANNEL option).</LI>
-                      <LI>A matrix_list file is output automatically when trainning matrices.</LI>
-                   </UL>
-                </LI>
-                <LI>Example
-	        <PRE><b>EXAMPLE:</b> seq_reformat -in myseq.fasta -action +pavie_seq2pavie_aln pavie_matrix.cycle_1.mat_list _ID02_</PRE></LI>
-             </UL>
-
-       <LI><H3><FONT COLOR="#8B4513">Transition Matrices</FONT></H3></LI>
-            <UL>
-                <LI>Given a series of sequences, one can compute the log odd associated with transitions:
-                <PRE><b>EXAMPLE:</b>seq_reformat -in myseq.fasta -output transitions</i>|</PRE></LI>
-            </UL>
-
-        <LI><H3><FONT COLOR="#8B4513">Tutorial and examples</FONT></H3></LI>
-        <LI><H3><FONT COLOR="#8B4513">Related Links</FONT></H3></LI>
-        <LI><H3><FONT COLOR="#8B4513">Contact</FONT></H3></LI>
-        Email   :  <A MAILTO="cedric.notredame@europe.com">cedric.notredame@europe.com</A>    <br>
- 
-      </UL>
-       
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